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- # <code>/home/pren/bin/density.sh some.xyz</code> is a shell script to compute density for a ...or converting between dcd and archive/xyz, extract frames, etc See <code>~pren/tinker8/2604/bin</code> ...569 bytes (99 words) - 20:29, 8 April 2026
- example mdin and run script files in /home/pren/AMOEBA/solvation/compare/ /opt/mpich2-fc7/bin/mpirun -n 4 /home/pren/pmemd-oscar/src/pmemd -i ele.mdin -c ele.inpcrd -p ele.prmtop -o mdout.nvt. ...2 KB (329 words) - 23:30, 21 April 2025
- ...l source is in /home/pren/DARDEN_amber An example compiled on pluto: /home/pren/AMOEBA/amber-range-soft === ''''' Tom's orginal instruction in ~pren/DARDEN_amber/README''''' === ...4 KB (556 words) - 23:32, 21 April 2025
- ~pren/poltype-1.1.3-dev/poltype.py.0.1 -s *.sdf -n 8 -m 6000MB -M 120GB --do-tor- ...311 bytes (38 words) - 23:07, 21 April 2025
- /home/pren/tinker5-2-2009/source/poledit.x 1 gdout /home/pren/tinker5-2009-6/source/poledit.x 1 gdout < poledit.input ...3 KB (460 words) - 23:26, 21 April 2025
- cp /home/pren/tinker9/run.sh.r9 . export CMAKEHOME=/home/pren/Software/cmake-3.28.0/bin ...4 KB (628 words) - 16:35, 11 October 2024
- *move multipoles to offisite using movepole.f in ~pren/tinker/tinker-bat/ ...2 KB (329 words) - 23:35, 21 April 2025
- (a test dire: /home/pren/AMOEBA/solvation/cresol/vdw0.4)<br> ...effect. Oscar, can you confirm this contribution is indeed small? In /home/pren/AMOEBA/solvation/cresol/vdw0.4 I set up an example for a single NMA, and pr ...7 KB (1,264 words) - 23:34, 21 April 2025
- Pengyu Ren pren@utexas.edu UT Austin ...4 KB (355 words) - 15:06, 16 June 2024
- '''Organizers''': Pengyu Ren (pren@mail.utexas.edu); Jay Ponder (ponder@dasher.wustl.edu); Jean-Philip Piquema http://biomol.bme.utexas.edu/~pren/TinkerMeeting/2018/menu/Breakfast%20Cafe%20125%20Menu.pdf ...11 KB (1,438 words) - 03:32, 10 May 2022
- /home/pren/tinker/bin/analyze<br> Only analyze from TINKER4.3 work for now (/home/pren/tinker/bin ...11 KB (1,882 words) - 23:13, 21 April 2025
- ...f the fftw library''' above. In Makefile make the following changes (/home/pren/tinker6/source-2014-xz-node/Makefile). You also need to remove any "$( ...5 KB (760 words) - 18:00, 19 September 2023
- |pren@utexas.edu ...5 KB (687 words) - 15:49, 18 November 2024
- *Use parameters from /home/pren/AMOEBA **/home/pren/AMOEBA/amoeba_v2_new.prm ...9 KB (1,234 words) - 23:11, 21 April 2025
- source ~pren/amber-git/amber17/bashrc.amber16 source /home/pren/amber-git/amber17/ambercpu/amber.sh ...11 KB (1,642 words) - 21:40, 30 August 2022
- * You can now use ~pren/avgmpoles.pl extracted_key first_atom_type last 1 new_key to average mutipo =Note please use tinker 4.3 parameter style and executable (in ~pren/tinker4.3) if you want to use with AMBER.= ...11 KB (1,698 words) - 23:14, 21 April 2025
- https://biomolmd.org/pren/nodes.html ...or:#ffff33;">Complete CPU/GPU usage & sign up spreadsheet</span> '''(email pren to request permission to edit): [https://docs.google.com/spreadsheets/d/1EO ...9 KB (1,537 words) - 14:59, 17 October 2025
- *Distance restraint is not working with the current pmemd.amoeba (see /home/pren/pmemd-oscar/readme) example mdin and run script files in /home/pren/AMOEBA/solvation/compare/ ...52 KB (7,895 words) - 23:03, 21 April 2025
- Installation files: ~pren/forcebalance-installation/ source ~pren/.cshrc.force ...80 KB (11,943 words) - 23:01, 17 December 2024
- python setup.py install --user --install-scripts ~pren/bin ~pren/bin/propka31 1hpx.pdb ...90 KB (14,245 words) - 23:21, 7 July 2022