- Click here to go back to Pengyu Ren Lab website
- Click here to go to POLTYPE ligand parameterization tool
- Links to the other Tinker platform:
A high performance software for molecular model and design. Running Molecular Dynamics using AMOEBA force field and OpenMM GPU engine through TINKER-OpenMM interface. You will be able to run Molecular Dynamics simulations with the regular TINKER inputs and ouputs using the OpenMM as the backend engine.
Download and Install cuda driver and library (this will install the Nvidia driver). Usually install into /usr/local/cuda. Currently we are using cuda_7.5 but 6.5 should also work.
Download OpenMM (forked from Pande group, with modifications). Tips for installing this version of openmm: http://biomol.bme.utexas.edu/wiki/index.php/Research_ex:Openmm#Installation
Download tinker with openmm interface:
Intel compilers are recommended.
Compile tinker/source as usual.
Compile dynamic_omm.x by copying files from tinker/openmm/ into tinker/source. You need to modify the Makefile and replace with your own openmm directory
OPENMMDIR = /users/mh43854/openMMstable2/bin Example source file for running dynamic_omm export PATH=$PATH:/usr/local/cuda-7.5/bin/ export LD_LIBRARY_PATH=/usr/local/cuda-7.5/lib64:/usr/local/cuda-7.5/lib:$LD_LIBRARY_PATH export CUDA_HOME=/usr/local/cuda-7.5/ export LD_LIBRARY_PATH=/users/mh43854/openMMstable2/bin/lib:$LD_LIBRARY_PATH export PATH=/users/mh43854/openMMstable2/bin/:$PATH export OPENMM_PLUGIN_DIR=/users/mh43854/openMMstable2/bin/lib/plugins export OPENMM_CUDA_COMPILER=/usr/local/cuda-7.5/bin/nvcc export CUDA_VISIBLE_DEVICES=0
Now you can run dynamic_omm.x as the usual dynamic.x but it will use GPU instead of CPU.
- AMOEBA force fields and tinker inputs (same as those for CPU version)
- Bussi thermostat
- RESPA (2fs) integrator. 3fs is possible if using H mass re-partitioning.
- Cubic PBC
- 4-5 ns/day for the DHFR (JAC) benchmark system on GTX970 (cuda 7.5).
- Softcore vdw and scaled electrostatics for free energy calculations.
- NPT is possible with Monte Carlo barostat ("Barostat MONETECARLO" in key file). However, the most reliable NPT is available on CPU using Nose-Hoover integrator/thermostat/baraostat (1 fs time-step).
- centroid based distance restraint, torsion restraint
Work in progress:
- AMOEBA virial and constant pressure
Example tinker key file
parameters amoebapro13.prm integrator RESPA #respa integrator allows 2-fs time step; 3fs with H mass repartitioning thermostat BUSSI barostat montecarlo ewald neighbor-list vdw-cutoff 12.0 ewald-cutoff 7.0 polar-eps 0.00001 polar-predict archive #pme-grid 72 72 72 #grid can be set automatically by TINKER/OpenMM; if set manually, it should be at least 1.1 x box size and allowed values are in kewald.f a-axis 56.050244 #BONDTERM only #ANGLETERM only #UREYTERM only #OPBENDTERM only #TORSIONTERM only #ANGTORTERM only #VDWTERM only #MPOLETERM only #POLARIZETERM only #verbose #if above ucommented ("verbose" enabled); tinker will print both CPU and GPU energy of the initial structure for comparison before MD starts. Suggested for testing before long simulations #Also answer no if asked if you want send information from GPU back.
We have run the code on GTX780, 970 and 980. Testing on GTX1070 is in progress.