View source for Lab:labinfo


= Welcome, Ren Lab Members! =

&nbsp;

== General&nbsp;Information ==

=== Lab Website ===

[https://biomol.bme.utexas.edu/ https://biomol.bme.utexas.edu/] &nbsp;

=== Lab Office Number ===

'''BME 3.516''' 

=== How to Find Lab ===

* Go to the 3rd floor of BME (ground floor on Dean Keeton side, next floor up on the South side)
* There is a hallway on the west side of the building that runs north-south
* if you come in from the lobby it is on the right side of the building running straight back
* the last door at the end of the hallway (located near Stair 3)

=== Dr. Ren's Office Number ===

'''BME 5.202M''' (located in 5th floor faculty suite)

== Communication and File Sharing ==

=== Slack ===

*utren.slack.com 
*accounts will be created for new lab members/rotation students 
*noteworthy channels
*##software for discussing various lab software + issues
*##cat for sending cat pics
*##paper-literature for sharing helpful papers + interesting new general papers
*##amoebaplus
*##poltype
*##general - general Ren lab stuff
*##allinclude - basically general but including some Schnieders lab members

=== Lab Contacts ===
https://docs.google.com/spreadsheets/d/1Lea3_EAsVyOcMja7Ox_mNfj8ZNzj6Dupd8w5dNuFr4I/edit?usp=sharing

=== Lab Meetings ===

https://docs.google.com/spreadsheets/d/133vg99syg17xPR-H-UH0B2gLlC9469AFAwMQx2LGn4s/edit?usp=sharing

=== Individual Meetings ===

[https://docs.google.com/spreadsheets/d/1yLw5xenlOgIdsylFVk4fDnu7s5juZvgFgU8ztYvMfQE/edit?pli=1#gid=0 https://docs.google.com/spreadsheets/d/1yLw5xenlOgIdsylFVk4fDnu7s5juZvgFgU8ztYvMfQE/edit?pli=1#gid=0] &nbsp;

=== Cluster Sign-Up Sheet ===

[https://docs.google.com/spreadsheets/d/1EOlUwFpdNU2uBZ5XrHSvZnRYCUCOw5tCSkFisTm3big/edit?pli=1#gid=0 https://docs.google.com/spreadsheets/d/1EOlUwFpdNU2uBZ5XrHSvZnRYCUCOw5tCSkFisTm3big/edit?pli=1#gid=0]&nbsp;

=== AMMM Meeting Sign-Up Sheet (Summer) ===
https://docs.google.com/document/d/1Pn2ZhHBQ82miVhl6CGG0zj2rMQxTLvTznrGColcNYhQ/edit?usp=sharing

=== Suggested Literature (in Box) ===

[https://utexas.app.box.com/folder/103794407727 https://utexas.app.box.com/folder/103794407727] &nbsp;

== Learning and reading ==
You are expected to learn from your labmates and by reading literature regularly. Most learnings in grad school/postdoc training are not from classroom!

You will run MD simulations and free energy calculations, using polarizable force field AMOEBA. These are expertise our lab has developed over past two decades so anyone to graduate from this lab should understand how and why on the following relevant subjects. You all should spend time read papers and documents I have been sharing. If you don't understand what you do and only run others' scripts to get numbers, you won't go far.
* Polarizable multipole force field AMOEBA. why and how
** Understand AMOEBA model (read slides and latest review paper Jing et al)
** Using POLTYPE to get parameters and understand what POLTYPE is doing (read POLTYPE papers)
* Hydration free energy. Salt effect and charge correction (if solute has net charge)
** FEP and BAR
** Other methods including TI and WHAM (PMF)

* Binding free energy calculations
** restraint and standard state correction
** Neutralizing counter ion and background salt; what to do when ligand has net charge
** It is OK to use other's script (Brandon, CW) to set thing up and learn. But you need to know what the program is doing, how and why again.
* How to compile Tinker CPU and GPU code

* Advanced models/enhanced sampling methods
** AMOEBA+
** AI based models
** Adaptive biasing force (ABF)
** Metadynamics (well tempered)
** OSRW
** few years ago our lab members did a seminar course together and covered a wide range of topics: https://biomol.bme.utexas.edu/wiki/index.php?title=Course:ABS

Many topics above found on lab wiki (https://biomol.bme.utexas.edu/tinkergpu) and a BOX folder I shared with lab members (for example AMOEBA folder has slides and papers introducing AMOEBA). If you don't have/see anything or have question, contact asap. 
It is important to establish a routine, setting aside time to read regularly (daily, weekly). I would start from basic and whatever relevant to what you are doing now and gradually cover more and more.




= Lab policy & resource =


=== Financial support ===

PhD students are typically fully supported via either GRA ot TA. However funding is not always guaranteed. Studenst and postdocs are expected to work deligently and be productive, which in turn will help us to secure the funding to support your stipend, fringe, tuition and other expense.


=== Work schedule ===

Postdocs are required to fill in time sheet per university policy. While we don't require everyone follow a fixed schedule, everyone is expected to follow "reasonable" working hours (e.g. 9am - 5pm). People who show chronic tardiness and fail to comply after multiple warnings will be asked to leave.

=== Vocation and leave  ===
Graduate students and postdocs are supported by either state or federal funds (including TA and RA ship). You are considered employees (hence the benefit etc.). We typically observe the university official holiday and vacation policy (http://www.utexas.edu/hr/holiday/ and http://www.utexas.edu/hr/current/leave/annual.html). You are allowed to take 4 weeks off for vacation each year, holidays and sick days not included. '''Please consult with PI in advance to plan on a vacation.''' 

Please note'''Winter, spring and summer breaks are NOT vacation time'''. These are breaks for classes and undergraduate students, not for staff and employees. You can certainly take vacations during the breaks (use against the 4-week a year vacation time).

You need to consult with PI for longer/extended leave. You may not expect financial support for the extended leave. 

We expect students to respect the rules and work diligently, which is essential for us to to receive funding to support everyone in the lab.

=== Lab Resource ===

When use the cluster, be considerate. Don't spread your job all over the nodes (use all the processors on one node before using other nodes), so that others that need the multiprocessors can utilize them.

CPU & GPU resources in the lab (email Dr. Ren if you need write permission) https://docs.google.com/spreadsheets/d/1EOlUwFpdNU2uBZ5XrHSvZnRYCUCOw5tCSkFisTm3big/edit#gid=0

More about using the cluster: https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Tinkergpu:Newuser

=== Lab Responsibility ===

Each of you will share some lab responsibility, such as maintenance, purchasing, organizing group meeting etc. Senior lab members are expected to advise and help out new lab members on research.

=== Lab security  ===

* Do not use university resource for personal use.

* Do not install or alter operating system and software, change system setting or have root privileges (including sudo) on lab computers/workstations/laptops, unless with explicit permission from PI.

* You are responsible to make sure your workstation and user account (password) are secure. 

* The university monitors the internet activity of every network port. 

<br>Always lock the door when you are the last one to leave.

=== Meetings and Conference  ===

*Funding

The lab provides support for each of you to go to meetings and conferences to present your work in orals or posters. The amount ($500 - $1000 a year) depends on funding availability and your presentation (oral has higher priority) etc. You are also strongly encouraged to seek for support from department, college and society etc, many in the format of award. 

Oral presentations receives a higher priority for support than posters.

*Save all your receipts and program documents etc.
*Send me the following in electronic format (word doc, PDF) 
**Your abstract before submission for me to check 
**Published abstract (web print or scanned pdf)
**Official program page that has your presentation or poster title and author names (web print or scanned pdf is fine).
**The final powerpoint files for presentation or poster
===Graduate students fellowships===
http://www.grad.nd.edu/gfd/

http://www.lib.msu.edu/harris23/grants/3gradinf.htm#a

= Technical reading materials =


== Molecular Modeling ==

 Book: Molecular Modelling, Principles and Pllications, Andrew Leach
 Computer simulations of liquids, Allen & Tildesley
 Book: Molecular Simulations, Frenkel and Smit

You can use Google to find these books online.

&nbsp;

== Free energy ==

Book:

 '''Free energy Calculations, Theory and Applications in Chemistry and Biology''', Chipot and Pophorille, Springer

Review by Simonson & Roux (charge correction/solution-gas-phase): Concepts and protocols for electrostatic free energies

 [https://utexas.box.com/s/fx8ixqhz9zj9i5ebv3rzrgclwiighnd6 https://utexas.box.com/s/fx8ixqhz9zj9i5ebv3rzrgclwiighnd6]

More about charge corrections when system/ligand being disappeared is not neutral

 [https://utexas.box.com/s/nj6jcufmms5hs1xqu5pywkwp3kax3y6k https://utexas.box.com/s/nj6jcufmms5hs1xqu5pywkwp3kax3y6k]

== Force Fields ==

MSI force field handbook:&nbsp;

&nbsp;[https://utexas.box.com/s/ge7f4q6svq5ammy736c7d729ms6jxzzw https://utexas.box.com/s/ge7f4q6svq5ammy736c7d729ms6jxzzw]

== Molecular binding termodynamics & simlations ==

Gilson & Zhou

  [https://utexas.box.com/s/esttb5govnir7mvnvydcid4ukv7nxmnc https://utexas.box.com/s/esttb5govnir7mvnvydcid4ukv7nxmnc]
  [https://utexas.box.com/s/dugh8ba95gf8v0fnsnzf6a63beu47qee https://utexas.box.com/s/dugh8ba95gf8v0fnsnzf6a63beu47qee]
  [https://utexas.box.com/s/p2fcjdzdssuxicopv5mkl843grrjinoh https://utexas.box.com/s/p2fcjdzdssuxicopv5mkl843grrjinoh] 

Hamelberg & McCammon

  [https://utexas.box.com/s/bsayz0jmfgd7o8ibx0pqtkoqwuk108tm https://utexas.box.com/s/bsayz0jmfgd7o8ibx0pqtkoqwuk108tm]

Ren lab:

  [http://www.pnas.org/content/pnas/105/17/6290.full.pdf http://www.pnas.org/content/pnas/105/17/6290.full.pdf]

== Data analysis ==

 R for Data Science: [http://r4ds.had.co.nz/ http://r4ds.had.co.nz/]

= Writing =

== Writing a scientific paper, step by painful step by Kevin D. Lafferty ==

  [http://trophiccascades.forestry.oregonstate.edu/sites/trophic/files/Lafferty_WritingScientificPaper.pdf http://trophiccascades.forestry.oregonstate.edu/sites/trophic/files/Lafferty_WritingScientificPaper.pdf] 

== Recipe for a Quality Scientific Paper: Fulfill Readers&nbsp;and Reviewers&nbsp;Expectations ==

 Prof Yaoqi Zhou [https://utexas.box.com/s/m93b92gwzcxgi1iw8qw7gdf6z7duzmm1 https://utexas.box.com/s/m93b92gwzcxgi1iw8qw7gdf6z7duzmm1] 

== Making better figures ==

  [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003833 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003833]

== 21 suggestions ==

 [https://www.scitechedit.com/images/21_writing_tips.pdf https://www.scitechedit.com/images/21_writing_tips.pdf] 

== Ten simple rules for structuring papers ==

 [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005619 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005619]

&nbsp;

= Literature search =

pubmed:&nbsp;[https://www.ncbi.nlm.nih.gov/pubmed/ https://www.ncbi.nlm.nih.gov/pubmed/]&nbsp;

Web of science (use UT eid when off campus):&nbsp;[https://guides.lib.utexas.edu/az.php?a=w https://guides.lib.utexas.edu/az.php?a=w]&nbsp;

Hot paper search&nbsp;[https://www.oligotherapeutics.org/hot-papers-search/ https://www.oligotherapeutics.org/hot-papers-search/]

Off campus access&nbsp;to paper download&nbsp;via ezproxy:&nbsp;[https://legacy.lib.utexas.edu/help/proxy.html#subscription https://legacy.lib.utexas.edu/help/proxy.html#subscription]

Check out resources (including classes) offered by university library

= Presentation =

<span style="font-family:"><span style="color:#1f497d">[http://blogs.nature.com/naturejobs/2017/01/11/scientific-presentations-a-cheat-sheet/ http://blogs.nature.com/naturejobs/2017/01/11/scientific-presentations-a-cheat-sheet/]</span></span>

<span style="font-family:"><span style="color:#1f497d">[http://www.nextscientist.com/improve-presentation-skills-of-phd-students/ http://www.nextscientist.com/improve-presentation-skills-of-phd-students/]</span></span>

&nbsp;

= Graduate and Postdoc Fellowship =

<span style="background:white"><span style="font-size:10.5pt"><span style="font-family:"><span style="color:#222222">NSF, [https://www.nsfgrfp.org/ https://www.nsfgrfp.org/]</span></span></span></span>

<span style="background:white"><span style="font-size:10.5pt"><span style="font-family:"><span style="color:#222222">NIH, [https://researchtraining.nih.gov/programs/fellowships/f31 https://researchtraining.nih.gov/programs/fellowships/f31]</span></span></span></span>

<span style="font-size:10.5pt"><span style="font-family:"><span style="color:#222222">America Heart Association [https://professional.heart.org/professional/ResearchPrograms/ApplicationInformation/UCM_443316_Predoctoral-Fellowship.jsp https://professional.heart.org/professional/ResearchPrograms/ApplicationInformation/UCM_443316_Predoctoral-Fellowship.jsp]</span></span></span>

SAMRT:&nbsp;[https://www.asee.org/fellowship-programs/graduate https://www.asee.org/fellowship-programs/graduate]&nbsp;

NDSEG&nbsp;[https://ndseg.asee.org/ https://ndseg.asee.org/]&nbsp;

&nbsp;

== Fellowship Databases: ==

[http://www.grad.nd.edu/gfd/ https://gradschool.cornell.edu/fellowships]&nbsp;

[http://www.lib.msu.edu/harris23/grants/3gradinf.htm#a https://awardsdatabase.usc.edu/]

[http://grad.berkeley.edu/news/headlines/guide-to-fellowships-grants/ http://grad.berkeley.edu/news/headlines/guide-to-fellowships-grants/]&nbsp;

= Career Development =

== The Professor Is In: The Essential Guide To Turning Your Ph.D. Into a Job==

 [https://www.amazon.com/Professor-Essential-Guide-Turning-Ph-D/dp/0553419420 https://www.amazon.com/Professor-Essential-Guide-Turning-Ph-D/dp/0553419420]

 Some contents are inspired by&nbsp;[https://twitter.com/thehauer/status/1021179403680862218?s=19 https://twitter.com/thehauer/status/1021179403680862218?s=19] 
== Communication kit ==

nstructions on writing cover letters, formatting CVs, writing abstracts, personal statements, etc.

[http://mitcommlab.mit.edu/be/use-the-commkit/ http://mitcommlab.mit.edu/be/use-the-commkit/]

== Lab Resources ==

===Disk spaces ===
Your home dir is in /home/YOURUSERNAME, which is physically on Nova and space is limited. But each of you have space in /work/YOURUSERNAME (physically on SUN), which is at least 2 TB (more if needed). You can access home and work dir similarly on all computers in the lab. If you have MD jobs producing large trajectories and you wan to keep them for analysis (until paper pub), please use /work. You can check your space and quota limits in /opt/quota.* Once you reach quota you can not log in or execute commands.
===Using Lab Cluster===
[[Lab:newuser| new user set up to access lab cluster]]

=== Cluster Monitoring ===
https://biomol.bme.utexas.edu/~pren/nodes.html 

[https://docs.google.com/spreadsheets/d/1EOlUwFpdNU2uBZ5XrHSvZnRYCUCOw5tCSkFisTm3big/edit?usp=sharing CPU & GPU resource sign up]

=== GPU Monitoring ===

[https://biomol.bme.utexas.edu/~rq875/checkgpu.log https://biomol.bme.utexas.edu/~rq875/checkgpu.log] &nbsp;

=== Tinker Tutorials ===

[https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Tinkergpu:Tinker-tut https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Tinkergpu:Tinker-tut] &nbsp; &nbsp;

=== Poltype Github ===

https://github.com/TinkerTools/poltype2

=== Linux Utilities ===

[https://docs.google.com/document/d/1cnmSItdRXDBcpVBGhwDahJVJ2jeh4l2oDVpMBLtlySE/edit https://docs.google.com/document/d/1cnmSItdRXDBcpVBGhwDahJVJ2jeh4l2oDVpMBLtlySE/edit] &nbsp;

=== Lab Guide for Grad Students ===

[https://docs.google.com/document/d/1PKyWNTntusPeRrOiGaLAkUvJbuuc4cVBfE4Lo9ZMt2I/edit https://docs.google.com/document/d/1PKyWNTntusPeRrOiGaLAkUvJbuuc4cVBfE4Lo9ZMt2I/edit] &nbsp; &nbsp;

== UT Resources ==

=== Ombuds ===

*[https://ombuds.utexas.edu/student/about-us https://ombuds.utexas.edu/student/about-us] 
*Can listen to your concerns, give advice, and direct you to resources 

=== Employee Assistance Program ===

Counseling

*[https://eap.utexas.edu/counseling-consultations https://eap.utexas.edu/counseling-consultations]&nbsp; 

Wellness (sometimes has fitness videos)

*[https://healthpoint.utexas.edu/ https://healthpoint.utexas.edu/]&nbsp; 

=== Night rides (Lyft discount) ===

*[https://parking.utexas.edu/night https://parking.utexas.edu/night]&nbsp; 

=== University Health Services ===

*List of services [https://www.healthyhorns.utexas.edu/appointments.html#services https://www.healthyhorns.utexas.edu/appointments.html#services]&nbsp; 
*As employees, a lot of care is free. Sometimes there is a copay, but it is very affordable usually 

COVID testing

*[https://www.healthyhorns.utexas.edu/coronavirus_testing.html https://www.healthyhorns.utexas.edu/coronavirus_testing.html]&nbsp; 

Women’s Health

*[https://www.healthyhorns.utexas.edu/womenshealth.html https://www.healthyhorns.utexas.edu/womenshealth.html]&nbsp; 

Free nurse advice line

*[https://healthpoint.utexas.edu/247-nurse-line https://healthpoint.utexas.edu/247-nurse-line]&nbsp; 

=== Student Emergency Services ===

Services offered [https://deanofstudents.utexas.edu/emergency/howwecanhelp.php https://deanofstudents.utexas.edu/emergency/howwecanhelp.php]&nbsp;

Student Emergency Fund

*[https://deanofstudents.utexas.edu/emergency/studentemergencyfund.php https://deanofstudents.utexas.edu/emergency/studentemergencyfund.php]&nbsp; 

=== Services for Students with Disabilities ===

*[https://diversity.utexas.edu/disability/about/ https://diversity.utexas.edu/disability/about/]&nbsp; 
*The process is a bit difficult sometimes, be aware 

== Life in Austin ==

=== Coffee Shops ===

*[https://goo.gl/maps/4nDa3AMZDFoTA9FTA https://goo.gl/maps/4nDa3AMZDFoTA9FTA] 

=== Food ===

*[https://goo.gl/maps/v4fQHJ4YhYtMrNh29 https://goo.gl/maps/v4fQHJ4YhYtMrNh29]&nbsp; 

=== Essential Stores ===

*[https://goo.gl/maps/iTLRvaAf4anVkm7j6 https://goo.gl/maps/iTLRvaAf4anVkm7j6]&nbsp; 

&nbsp;

=== Outdoor Landmarks / Hiking ===

Highest point in Austin, not much of an actual hike

*[https://goo.gl/maps/nd2aAXqoyVPivADH6 https://goo.gl/maps/nd2aAXqoyVPivADH6]&nbsp; 

Pennybacker Bridge (park on side of road, can go up either side of road)

*[https://goo.gl/maps/zfYHwUkRTYwTQfu69 https://goo.gl/maps/zfYHwUkRTYwTQfu69]&nbsp; 

Overlook&nbsp;Trail (3ish miles each way, nice overlook part way, decent elevation change)

*[https://goo.gl/maps/Cx9YdkuQWWmKBGAe9 https://goo.gl/maps/Cx9YdkuQWWmKBGAe9]&nbsp; 

Bat Observation

*[https://goo.gl/maps/ZHfnn54qKY6icEq3A https://goo.gl/maps/ZHfnn54qKY6icEq3A] 
*Austin has a bat colony. The bats migrate but they like to hang out under the Congress bridge. 
*You can park in a paid lot or take the bus&nbsp;and watch the bats fly sometime around sunset. You can also watch the bats from the river or on top of the bridge. 
*It’s really neat and an Austin staple.&nbsp;Sometimes there are a lot of people. 

Parks to wander around near campus

*[https://goo.gl/maps/fRs2w2LCX7emZNuWA https://goo.gl/maps/fRs2w2LCX7emZNuWA] 
*[https://goo.gl/maps/Vu7L1DZDevn1FXNG6 https://goo.gl/maps/Vu7L1DZDevn1FXNG6] 
*[https://goo.gl/maps/2qn9a8U1w3ZZY72u9 https://goo.gl/maps/2qn9a8U1w3ZZY72u9]&nbsp; 

=== Pet Care Resources ===

*Sometimes you can get pet supplies at the APA thrift stores 
*Austin is very dog friendly and has many dog parks 

Great web resources

*[https://www.austinpetdoctor.com/pet-education-center/ https://www.austinpetdoctor.com/pet-education-center/]&nbsp; 
*[https://goo.gl/maps/SHm6N2Xgrdptcfsx7 https://goo.gl/maps/SHm6N2Xgrdptcfsx7] 
*[https://goo.gl/maps/A4qmGfa6VQqomRFq9 https://goo.gl/maps/A4qmGfa6VQqomRFq9]&nbsp;