Re: [gmx-users] query for gromacs-4.5.4

Hello Sir, Actually I have been given work to setup gromacs-4.5.4 in our cluster which is being used by users.I am not gromacs user and not aware of its internal details. I have got only .tpr file from user and I need to test my installation using that .tpr file. It works fine for 2 nodes 8 proce

[gmx-users] removing rotational and translational motion (holonomic contraint)

Hi guys I am running a set of umbrella sampling simulations using gromacs 333 and the "pull" code. The idea is to apply an umbrella potential to restrain the distance between a protein and a ligand in the x direction. Unfortunately, the rotational and translational movement of the protein durin

Re: [gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol for l-bfgs)

I printed all small 50 eigenvalues, and their first 9 are listed as follows as before:* -1.8476593e-06* -1.2164109e-06* -1.4830436e-07* 1.3104790e-06* 1.1364704e+00* 1.7418209e+00* 2.2836573e+00* 3.7218206e+00* 4.4875873e+00 As you see, the first three of them are negative and close to zero, whi

Re: [gmx-users] mdrun WARING and crash

On Monday, March 11, 2013, wrote: > Hallo Justin, > > Thank you for your comments. > Taking your suggestions, I set nrexcl=1, and comment the [pairs] section, > because there is no special case of non-bonded interactions to declare, > then we try to see what happens. > Now we minimize it by steep

RE: [gmx-users] mdrun WARING and crash

Hallo Justin, Thank you for your comments. Taking your suggestions, I set nrexcl=1, and comment the [pairs] section, because there is no special case of non-bonded interactions to declare, then we try to see what happens. Now we minimize it by steep, then by cg, both of the processor are very

[gmx-users] TMD using free energy code

Dear Gromacs users, I would like to perform targeted molecular dynamics with gromacs. I have read all the post concerning it and I can do it with position restraints by putting the final conformation in the -r option of grompp. But this is not a "real TMD". Indeed, in TMD, the force applied to the

Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

Hi, On Mar 11, 2013, at 10:50 AM, George Patargias wrote: > Hello > > Sorry for posting this again. > > I am trying to run GROMACS 4.6 compiled with MPI and GPU acceleration > (CUDA 5.0 lib) using the following SGE batch script. > > #!/bin/sh > #$ -V > #$ -S /bin/sh > #$ -N test-gpus > #$ -l

[gmx-users] Mismatching number of PP MPI processes and GPUs per node

Hello Sorry for posting this again. I am trying to run GROMACS 4.6 compiled with MPI and GPU acceleration (CUDA 5.0 lib) using the following SGE batch script. #!/bin/sh #$ -V #$ -S /bin/sh #$ -N test-gpus #$ -l h="xgrid-node02" #$ -pe mpi_fill_up 12 #$ -cwd source /opt/NetUsers/pgkeka/gromacs-4