[gmx-users] g_helix command error

Upon running g_helix_d -s md.tpr -n md.ndx -f md.trr -to gtraj1.g87 -cz zconf1.gro -co waver1.gro -b 0 -e 1000 -dt 1 -w -r0 1 -q -F -db -prop RAD -ev -ahxstart 1 -ahxend 28 I got the following output: Fatal error: rnr==0. Please tell me how can I proceed? Chitrita.

[gmx-users] No plot found running .xvg files using xmgrace produced by g_helix.

Dear gromacs user, I am stuck in a problem with g_helix command. The output of the g_helix is and a sample of the resultant .xvg files are attached here. There is no plot found when I ran resultant .xvg files by xmgrace. What are the problems here? Please help me out. Thanks in advance.

[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

I am performing grompp for md simulation after position restrained MD. Before final md simulation by grompp I have made pr.ndx file and did necessary corrections in it to insert added Na+ to be counted properly. But after running the following command - grompp -f md.mdp -c pr.gro -p scr8.top -o

Re: [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

Hi Tsjerk, Did you mean to send you the md.mdp file that I used to run grompp for md simulation? I am using Gromacs 4.0.2 versision. I am not very clear about the parameters used in mdp files. So I am sending the mdp file here. cpp = /usr/bin/cpp constraints =

Re: [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

Thanks a lot to both of you. Chitrita. On Wed, Mar 11, 2009 at 2:09 AM, Justin A. Lemkul jalem...@vt.edu wrote: Chitrita Dutta Roy wrote: Hi Tsjerk, Did you mean to send you the md.mdp file that I used to run grompp for md simulation? I am using Gromacs 4.0.2 versision. I am not very

[gmx-users] Parallel run on a Quad Core

Thanks to all for helping me previously. Now i am unable to arrange the .tpr file for position restraint mdrun on a quad core as in version 4.0.2 grompp -np is not a valid comand can anybody help me in building a tpr file for parallel run on 4 cores of a quad core machine .I have installed gromacs

Re: [gmx-users] Parallel run on a Quad Core

: Chitrita Dutta Roy wrote: Thanks to all for helping me previously. Now i am unable to arrange the .tpr file for position restraint mdrun on a quad core as in version 4.0.2 grompp -np is not a valid comand can anybody help me in building a tpr file for parallel run on 4 cores of a quad core machine .I

Re: [gmx-users] Parallel run on a Quad Core

, Chitrita Dutta Roy chitrita...@gmail.com wrote: Thanks to all for helping me previously. Now i am unable to arrange the .tpr file for position restraint mdrun on a quad core as in version 4.0.2 grompp -np is not a valid comand can anybody help me in building a tpr file for parallel run on 4 cores

Re: [gmx-users] Parallel run on a Quad Core

. On Sun, Dec 21, 2008 at 9:52 PM, Justin A. Lemkul jalem...@vt.edu wrote: Chitrita Dutta Roy wrote: I tried that way it basically creates 4 jobs and takes hold of 4 cpus but the problem is that it shows to take more time than it would normally without mpirun..and not only that a weird

Re: [gmx-users] Parallel run on a Quad Core

Sorry for the first step i used manual extraction as that was a bzip package. On Sun, Dec 21, 2008 at 10:05 PM, Chitrita Dutta Roy chitrita...@gmail.comwrote: tar -zxvf openmpi-1.2.8.tar.bz2 cd openmpi-1.2.8 ./configure make make install i had my fftw library installed. untarred gromacs

Re: [gmx-users] Parallel run on a Quad Core

Thanks for your help. ok i have gone through that and even the wiki dirty install.Ok i will go through those once more and will see if it works.Thanks once again. On Sun, Dec 21, 2008 at 10:15 PM, Justin A. Lemkul jalem...@vt.edu wrote: Chitrita Dutta Roy wrote: tar -zxvf openmpi-1.2.8

Re: [gmx-users] Parallel run on a Quad Core

But one thing as i did make links so definitely there are links of those executables in /usr/local/bin.How can i easily remove them..?? On Sun, Dec 21, 2008 at 10:15 PM, Justin A. Lemkul jalem...@vt.edu wrote: Chitrita Dutta Roy wrote: tar -zxvf openmpi-1.2.8.tar.bz2 cd openmpi-1.2.8

[gmx-users] Gromacs 4 with mpi interface

Can anyone give me a detailed notes on how to install gromacs 4 with mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as i am new to using gromacs plz give me as detailed note as possible.. And after adding some ions using genion when i try to run grompp again before final mdrun

Re: [gmx-users] Gromacs 4 with mpi interface

What exactly Do we need to change in the topology file suppose if we add 2 NA+ ions in the system..??? On Thu, Dec 18, 2008 at 1:45 AM, Justin A. Lemkul jalem...@vt.edu wrote: Chitrita Dutta Roy wrote: Can anyone give me a detailed notes on how to install gromacs 4 with mpi feature..I am

[gmx-users] Fatal Error: number of coordinates in coordinate file does not match topology

I want to perform MD Equilibration run under position restrained for 200ps. Bond distances were constrained using the LINCS (Linear Constraints) algorithm, the water molecules were restrained using the SETTLE algorithm. In order to do this I have modified nsteps in original pr.mdp file. Following