[gmx-users] Analysis of the RMSF of a ligand bound protein structure

Dear all, I am performing MD simulation on a ligand bound dimeric protein structure in Gromacs 5.04. For the calculation of RMSF of this dimeric protein I have used the following command gmx rmsf -s md_0_1.tpr -f md_0_1_traj.xtc -res -o rmsf_res.xvgand selected 'C alpha' group. But the

Re: [gmx-users] Problem with the MDS extended trajectory in Gromacs 5.04

jalem...@vt.edu wrote: On 7/9/15 3:09 PM, PAULAMI CHATTERJEE wrote: I have used the following commands for the initial mdrun gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr gmx mdrun -deffnm md_0_1 Can you please suggest now what went wrong? So you have a trajectory

[gmx-users] (no subject)

Dear All, I have a 30 ns trajectory which I would like to extend up to 100 ns. For that I gave the following commands gmx convert-tpr -s md_0_1.tpr -extend 7 -o final_monomer.tpr gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append After completion of the extension two new trajectory files

[gmx-users] Problem with the MDS extended trajectory in Gromacs 5.04

Dear All, I have a 30 ns trajectory which I would like to extend up to 100 ns. For that I gave the following commands gmx convert-tpr -s md_0_1.tpr -extend 7 -o final_monomer.tpr gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append After completion of the extension two new trajectory files

Re: [gmx-users] Problem with the MDS extended trajectory in Gromacs 5.04

: On 7/9/15 4:15 AM, PAULAMI CHATTERJEE wrote: Dear All, I have a 30 ns trajectory which I would like to extend up to 100 ns. For that I gave the following commands gmx convert-tpr -s md_0_1.tpr -extend 7 -o final_monomer.tpr gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append After

Re: [gmx-users] Problem with the MDS extended trajectory in GROMACS 5.0.4

Soumadwip Thank you very much for your response. So you are suggesting that   'gmx mdrun -s final_monomer.tpr -v -deffnm md_0_1 -cpi md_0_1.cpt -append' instead of 'gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append' (which I have used for the extended simulation) can solve my problem. I

[gmx-users] Installation problem with Gromacs 5.0.2

Dear all I am trying to install Gromacs 5.0.2 in a GPU machine but coming up with a CMake error. Part of my error looked like this . Downloading: http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz -- [download 0% complete] CMake Error at tests/CMakeLists.txt:58

Re: [gmx-users] Installation problem with Gromacs 5.0.2

, install and manually set the path in Cmake configuration. Good luck On Wed, Dec 10, 2014 at 5:10 PM, PAULAMI CHATTERJEE chatterjee_paul...@yahoo.co.in wrote: Dear all I am trying to install Gromacs 5.0.2 in a GPU machine but coming up with a CMake error. Part of my error looked like