[gmx-users] Free energy calculation of

Dear gxm users, Now I am doing solvation free energy of a protein, I follow Sander Pronk's tutorial downloaded from Gromacs page. 1. How do I check system is equilibrated? 2. I run following command sh mklambdas.sh run.mdp topol.top equil.gro I got following error: mklambdas.sh: 12:

Re: [gmx-users] Problem with constraints in NVT calculations.

Hi Justin and all, Meanwhile, is it possible to implement a self-consistent FF from scratch? One example I came across is from the work by Ho and Striolo titled: Polarizability effects in molecular dynamics simulations of the

Re: [gmx-users] grompp Segmentation fault

On 10/13/14 10:42 PM, Nilesh Dhumal wrote: hello, I running grompp for simulation. I get Segmentation fault error. grompp -f 600.mdp -c cu.gro -p cu_btc_1.top -o 1.tpr checking input for internal consistency... processing topology... Segmentation fault Could any one tell what is the

Re: [gmx-users] regarding confout.gro

On 10/14/14 12:31 AM, RINU KHATTRI wrote: hello gromacs user i am working on protein ligand complex with popc membrane i am running production md in extended time (40 ns) i got some file i am using -noappend option i got confout.gro file in each extended time what is the use of this file if i

Re: [gmx-users] Problem with constraints in NVT calculations.

On 10/14/14 7:40 AM, Kester Wong wrote: Hi Justin and all, Meanwhile, is it possible to implement a self-consistent FF from scratch? One example I came across is from the work by Ho and Striolo titled: Polarizability effects

[gmx-users] Conserved energy (Conserved En.) in NVT simulation

Dear Mark and ALL, I am trying to calculate the conserved energy (H-tilde) in Bussi's stochastic velocity rescale algorithm (jcp,2007). In previous maillist, ‍Mark had mentioned that the conserved En. in ener file is the H in bussi's paper

Re: [gmx-users] Using Gpus on multiple nodes. (Feature #1591)

Thank you Mark for the reply, We use pbs for submitting jobs on our cluster and this is how I request the nodes and processors #PBS -l select=2:ncpus=8:mem=8gb:mpiprocs=8:ngpus=2:gpu_model=k20:interconnect=fdr Do you think the problem could be with the way I installed mdrun using Open MPI?

[gmx-users] How long run should be enough for Free Energy Calculation of a protein?

Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? Batsaikhan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] 2-D liquid

Hi users, I am trying to simulate 2-d liquids interacting with simple potential like Lennard-Jones potential. Can it be done by specifying pcoupletype = semiisotropic in the .mdp file? I mean enforcing a normal pressure in x-y direction while very high pressure in z direction to constrain the

[gmx-users] (no subject)

Hello, I am doing Molecular-Dynamic simulation of Protein-Ligand complex embedded in POPC lipid membrane. After energy minimizing of complex, I am facing problem with NVT equilibration step. mdrun crashed with following error: 12 particles communicated to PME node 4 are more than 2/3 times the

Re: [gmx-users] Using Gpus on multiple nodes. (Feature #1591)

Try: mpirun -npernode 2 -Trayder On Wed, Oct 15, 2014 at 8:42 AM, Siva Dasetty sdas...@g.clemson.edu wrote: Thank you Mark for the reply, We use pbs for submitting jobs on our cluster and this is how I request the nodes and processors #PBS -l