Re: [gmx-users] g_rdf dual core

Osmair Vital de Oliveira wrote: Hi Mark, I am using GNU/Linux and when I run g_rdf appear this menssage: 'Reading frame 0 time0.000' And nothing occur for long time... you probably have a broken compiler. Mark asked you to specify what installation you used. Downgrade to gcc 4.0 or

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

Christopher Stiles wrote: I get the following when running grompp: -bash-3.00$ grompp -f mdout_test.mdp -c SWNT_6_6_144.gro -p SWNT_6_6_144.top -o :-) G R O M A C S (-: God Rules Over Mankind, Animals, Cosmos and Such

[gmx-users] question regarding restraints

Hello users I am using the gromacs 3.3 with 43a1 force field. I am using a restraint force of 50 intially during the beginning of protein simulation in water, even after such a high value of restraint force i can see some major deviations in my structure during the simulation. My doubt is that

Re: [gmx-users] question regarding restraints

gurpreet singh wrote: Hello users I am using the gromacs 3.3 with 43a1 force field. I am using a restraint force of 50 intially during the beginning of protein simulation in water, even after such a high value of restraint force i can see some major deviations in my structure during the

Re: [gmx-users] restarting a run using tpbconv

N-J.M. Macaluso wrote: Hello, I am running a very long simulation, and the cluster I'm using has a wall time. I am using tpbconv to restart my simulations from a frame in the last run, but this doesn't seem to be working. When I analyze the second trajectory, the starting structure looks

Re: [gmx-users] restarting a run using tpbconv

This may be a trivial question, but how do you save velocities in this case? Would it be in the .mdp file or in the tpbconv command? Thanks for your help, Max On Jul 21 2007, David van der Spoel wrote: N-J.M. Macaluso wrote: Hello, I am running a very long simulation, and the cluster

Re: [gmx-users] restarting a run using tpbconv

I have 2690 frames in my .trr file. Will providing the energy file in tpbconv solve the problem? On Jul 21 2007, Yang Ye wrote: The velocity is in the trr file. How many frames you have in protein.trr? What's its last frame? You also need to supply the energy file to tpbconv. On 7/21/2007

[gmx-users] search page does not return mailing list posts after mid april 2007

The search engine for the mailing list does not currently index posts after some time in May 2007. Perhaps there is a cron.php job that previously indexed the site automatically but that this job has not been run since some time in may? Perhaps related to the hacker issue? I discovered