Eew947: Created page with "= sander of amber pre 9 or DARDEN-AMOBEA version = The original source is in /home/pren/DARDEN_amber An example compiled on pluto: /home/pren/AMOEBA/amber-range-soft source ~/.cshrc.f10 cd sander make sander Modified (by socar) source in /home/oscar/data2-oscar/amber_mod_org/ See here for detailed modification http://biomol.bme.utexas.edu/wiki/index.php/Research:Amber_modification

README file in the directory explain the process. Esstially cd S..."

2025-04-21T23:32:17Z

Created page with "= sander of amber pre 9 or DARDEN-AMOBEA version = The original source is in /home/pren/DARDEN_amber An example compiled on pluto: /home/pren/AMOEBA/amber-range-soft source ~/.cshrc.f10 cd sander make sander Modified (by socar) source in /home/oscar/data2-oscar/amber_mod_org/ See here for detailed modification http://biomol.bme.utexas.edu/wiki/index.php/Research:Amber_modification README file in the directory explain the process. Esstially cd S..."

New page

= sander of amber pre 9 or DARDEN-AMOBEA version =

The original source is in /home/pren/DARDEN_amber An example compiled on pluto: /home/pren/AMOEBA/amber-range-soft

source ~/.cshrc.f10
cd sander
make sander

Modified (by socar) source in /home/oscar/data2-oscar/amber_mod_org/

See here for detailed modification http://biomol.bme.utexas.edu/wiki/index.php/Research:Amber_modification

 

 README file in the directory explain the process. Esstially cd SRC/sander and make sander. Other exe won't compile but not needed.

'''Use intel compiler ver 9! and REDHL or centos 4 (bme-sugar).'''

''Doesn't work on centos 5. error:Invalid GNU version''

''Intel v 10 will compile but segfault when running on fc 7 or 8.'' ''   ''''(were able to compile amber-rang-soft on pluto using intel v10, fc8.; and run OK)''''' '''
 
{| cellspacing="1" cellpadding="1" border="1" style="width: 742px; height: 164px;"
|-
| style="text-align: center;" | Intel
| Platform 
| Compile 
| Simulation 
| Energy minimization 
|-
| style="text-align: center;" | v10 
| fc8(venus),fc7(neptune),centos5(nova),ranger 
| YES 
| YES 
| NO (prints 1st step, SEG error) 
|-
| style="text-align: center;" | v9 
| fc7,fc8,fc10,centos5 
| NO(Invalid GNU version) 
| N/A 
| N/A 
|-
| style="text-align: center;" | v9

| centos4(sugar)

| YES 
| YES 
| YES 
|}
 

{| width="908" cellspacing="1" cellpadding="1" border="1" align="center" style=""
|-
|
=== ''''' Tom's orginal instruction in ~pren/DARDEN_amber/README''''' ===

copy the g95_config.h into the unpacked SRC diectory as config.h

should be able to go into sander and just say make sander all the amoeba specific stuff in sander directory is named amoeba_adjust.f etc. i.e. amoeba_ prefix the worst of the connection to regular sander is in the list builder and the fft code which are both fast but impenetrable code

i include my intel_config.h also---sometimes this is a problem depending on your c compiler and your loader for intel compiler you could try one of the options in configure script in src. remember to set AMBERBUILDFLAGS=-DAMOEBA in the resulting config.h to turn on the amoeba code

 use icc in intel_config.h

extract mdcrd to pdb: /opt/amber7/exe/ptraj pepc.prmtop pepc.scrpt pepc.scrpt: trajin mdcrd trajout tra.pdb pdb 

|}

 

= pmemd/amber9 from bob duke =

orginal source in /home/pren/pmemd-oscar

Follow COMPILE.readme!

Definitely should work (priot to summer 2008) using intel v9 and RHEL/centos 4.

But you have to remove "–luuid" in config.h

Seems to also work with intel v10 and FC7 or 8.

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++

bme-sun (fc7) /home/pren/pmdmd-sun

run ./configure linux_em64t ifort mpich2 pubfft < in

remove uuid and add DAMOEBA in config.h (append "-DAMOEBA" to config.h line DEFINE_F90: "F90_DEFINES = -DFFTLOADBAL_2PROC -DAMOEBA")

intel v10
/opt/intel/mkl/8.1
/opt/mpich2

'''Compilation using /opt/mpichi2 (1.03) works but may need mpich2-fc7 (1.05) to run the actual mpdboot.'''

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

= sander in amber 9 =

The softcor and ion and mdin (taking parameters for ligands and lambda?) modification yet to be transferred to sander/amber9.

Research:compile amber - Revision history