Re: [gmx-users] soft-core and coulomb transformation

bharat v. adkar wrote: Hi David, I am keeping the subject same so that it is helpful to track in future :) On Sat, 10 Nov 2007, David Mobley wrote: Dear Bharat, OK, I went ahead and ran with your topologies using my own run scripts. My runs haven't finished yet, but looking at just

Re: [gmx-users] soft-core and coulomb transformation

Hi David, I am keeping the subject same so that it is helpful to track in future :) On Sat, 10 Nov 2007, David Mobley wrote: Dear Bharat, OK, I went ahead and ran with your topologies using my own run scripts. My runs haven't finished yet, but looking at just values from equilibrati

Re: [gmx-users] Parallel run on IBM p575 "poe mpi"

liu xin wrote: Hi guys, just a short question, this is how I run a 8np mpi-mdrun job on my machine: poe /home/usr/programs/gromacs331mpi/bin/mdrun -v -s 8np.tpr --procs 8 -nodes 8 -task_per_node 1 -single_thread yes -eager_limit 65535 -shared_memory but it is much slower than the 1np mode,

Re: [gmx-users] "cannot compute sizeof (int), 77" on AIX 5.3 PPC p575 (searched the list)

hi Christian thx for your reply, I've tried that before with the "--enable-thread" option of fftw, with no success, after I turned it off , the installation seemed OK to me. Yours Xin On Nov 9, 2007 1:21 AM, Christian Burisch <[EMAIL PROTECTED]> wrote: > Hi, > > did you try the solutions given

[gmx-users] Parallel run on IBM p575 "poe mpi"

Hi guys, just a short question, this is how I run a 8np mpi-mdrun job on my machine: poe /home/usr/programs/gromacs331mpi/bin/mdrun -v -s 8np.tpr --procs 8 -nodes 8 -task_per_node 1 -single_thread yes -eager_limit 65535 -shared_memory but it is much slower than the 1np mode, I havent used poe-mpi

Re: [gmx-users] force=nan in frame 0

dongsheng zhang wrote: Dear Mark, Thank you for your reply. I have used gromacs before. In fact, I have built this FF before, and using it successfully. My old computer was crashed, so I need to do it again. The potential energies looked fine in the md.log. Even I turn off all potentials. I stil

[gmx-users] force=nan in frame 0

Dear Mark, Thank you for your reply. I have used gromacs before. In fact, I have built this FF before, and using it successfully. My old computer was crashed, so I need to do it again. The potential energies looked fine in the md.log. Even I turn off all potentials. I still get the initial foce =

Re: [gmx-users] (no subject)

dongsheng zhang wrote: Hello, I have build my own FF for a copolomer. When I ran the program, I got KE is NaN. I checked the output file trr. I found the initial forces of all particles at frame 0 are infinite. Could anyone tell me why this happened? Where I might make a mistake? Thank you i

[gmx-users] (no subject)

Hello, I have build my own FF for a copolomer. When I ran the program, I got KE is NaN. I checked the output file trr. I found the initial forces of all particles at frame 0 are infinite. Could anyone tell me why this happened? Where I might make a mistake? Thank you in advance! Dongsheng _

Re: [gmx-users] Re:Re: Incomplete header: nr 3078 time 9408

Dechang Li wrote: >> start by testing the trajectory with gmxcheck > I did what you said. Following is the message: > > Reading frame3000 time 9254.000 Warning at frame 3077. Velocities for > atom 11896 are large (52568.4) > Warning at frame 3077. Velocities for atom 11896 are large (7.682

Re: [gmx-users] trjorder does not write trajectory file

Dmytro Kovalskyy wrote: It works fine for me under 3.3.1 - what command line are you issuing? trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5 Reading the source, both -nshell and -r enforce no trajectory output. Mark ___ gmx-users mailing

Re: [gmx-users] trjorder does not write trajectory file

Use the -na and -da flags. trjorder doesn't know how to order the molecules without these. -Justin > Quoting Dmytro Kovalskyy <[EMAIL PROTECTED]>: > > > > It works fine for me under 3.3.1 - what command line are you issuing? > > trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5 > > > > >

[gmx-users] Re:Re: Incomplete header: nr 3078 time 9408

>Send gmx-users mailing list submissions to > gmx-users@gromacs.org > >To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users >or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > >You can reach

Re: [gmx-users] trjorder does not write trajectory file

> It works fine for me under 3.3.1 - what command line are you issuing? trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5 > > -Justin > > Quoting Dmytro Kovalskyy <[EMAIL PROTECTED]>: > >> >> Trjorder does not write trajectory file, only nshell.xvg >> >> This is true for 3.3.2 and 3.3.1 ve

Re: [gmx-users] Incomplete header: nr 3078 time 9408

Dechang Li wrote: Dear all, I used Gromacs-3.3.1 to do a simulation. When it finished, I used command "g_dist" to calculate two groups distance VS time. But at time 9408ps, it stopped and showed " Incomplete header: nr 3078 time 9408". My simulation is 12ns longer. What is the problem

[gmx-users] Incomplete header: nr 3078 time 9408

Dear all, I used Gromacs-3.3.1 to do a simulation. When it finished, I used command "g_dist" to calculate two groups distance VS time. But at time 9408ps, it stopped and showed " Incomplete header: nr 3078 time 9408". My simulation is 12ns longer. What is the problem? How can I re