[gmx-users] Error in Umbrella sampling

Hello all, I have been running the umbrella sampling tutorial available on the bevan lab website. After the following steps: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep When I run the

[gmx-users] Charges non-bonded interaction values usage in different force fields

Dear all, Experimentally determined charges and non-bonded interaction values for ligand atoms ( Written in charmm) can be used directly in gromacs provided charmm27.ff ? or does it need any conversion to use it in gromacs based charmm27.ff? -- Gromacs Users mailing list * Please search

Re: [gmx-users] Charges non-bonded interaction values usage in different force fields

Can you perhaps kindly explain us how charges and non-bonded interaction values were experimentally determined? Dr. Vitaly V. Chaban On Tue, Jun 24, 2014 at 10:37 AM, Rj ra...@kaist.ac.kr wrote: Dear all, Experimentally determined charges and non-bonded interaction values for ligand atoms

Re: [gmx-users] Error in Umbrella sampling

On 6/24/14, 2:57 AM, Maziya Ibrahim wrote: Hello all, I have been running the umbrella sampling tutorial available on the bevan lab website. After the following steps: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr trjconv -s pull.tpr -f

Re: [gmx-users] Fwd: segmentation fault on gpus

hi Justin, Thanks, that makes sense, however I was able to use the same ligand toplogy files with earlier versions like gromacs 4.5.4 to simulate protein ligand complexes. I can simulate protein-ligand complexes with the current versions also but only for the crystal structures that have ligand

Re: [gmx-users] Fwd: segmentation fault on gpus

On 6/24/14, 12:14 PM, ram bio wrote: hi Justin, Thanks, that makes sense, however I was able to use the same ligand toplogy files with earlier versions like gromacs 4.5.4 to simulate protein ligand complexes. I can simulate protein-ligand complexes with the current versions also but only for

Re: [gmx-users] Fwd: segmentation fault on gpus

no , they are different protein-ligand complexes, the issues are with 1. the source one is from protein data bank and other is modelled protein 2. versions with older version i could simulate the modelled complex too On Tue, Jun 24, 2014 at 12:18 PM, Justin Lemkul jalem...@vt.edu wrote: On

Re: [gmx-users] Fwd: segmentation fault on gpus

shall i do only two tc-grps protein and non-protein? On Tue, Jun 24, 2014 at 12:18 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/24/14, 12:14 PM, ram bio wrote: hi Justin, Thanks, that makes sense, however I was able to use the same ligand toplogy files with earlier versions like

[gmx-users] question about installation of gmx on Cray linux

Dear Gromacs Developers and Experts: I noticed that the performance of gromacs on Cray linux clusters is only 36.7% of the normal. The following is the detail about the installation -- CC=gcc FC=ifort F77=ifort CXX=icpc

Re: [gmx-users] Hamiltonian Replica Exchange

I would think of using Replica Exchange with Solute Tempering in this case. Look at the paper as to how one can implement this in Gromacs (doi: 10.1002/jcc.21703). Without having more details I would suggest to you to scale the Hamiltonian of each replica such that the Helix bundles are always

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 122, Issue 103

Dear Dr. Vitaly V. Chaban, The charges and non-bonded interactions of Carbon monoxide are set to give approximate agreement with the experimental dipole quardrupole moments ( J.E. Straub, M. Karplus, Chemical Physics, 1991). According to this article, with the specific point charges and LJ

[gmx-users] proteins break up in simulation

Dear all,In my NPT explicit solvent simulation on the proteins with multiple chains, sometimes the protein can break up and its chains leave far from each other. We wonder if this is caused by the instability of the protein or improper simulation conditions. Could anyone give me some

[gmx-users] topology file

Hi, I have a few technical questions regarding creating the topology file by using the command g_x2top. I would like to use the following GROMACS's command: g_x2top -f device.gro -ff oplsaa -o device.top to convert the .gro file to .top. The problem that I have is that the force field for

Re: [gmx-users] question about installation of gmx on Cray linux

Yes. Please start by reading the reply Justin made a few days ago. Your normal is unknown to us. Mark On Jun 24, 2014 10:29 PM, Tom dna...@gmail.com wrote: Dear Gromacs Developers and Experts: I noticed that the performance of gromacs on Cray linux clusters is only 36.7% of the normal.

Re: [gmx-users] Hamiltonian Replica Exchange

Indeed. REST implemented in PLUMED seems a good bet. Mark On Jun 24, 2014 11:50 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: I would think of using Replica Exchange with Solute Tempering in this case. Look at the paper as to how one can implement this in Gromacs (doi: