Re: [gmx-users] output energies by group

Hi Yuguang, you don't have to wait your mdrun job to finish to check out your energies,trajectories. Just use "g_energy" and you'll get the energies up to the last frame wrote on .edr file. Diego Enry. On 8/4/06, Mu Yuguang (Dr) <[EMAIL PROTECTED]> wrote: Dear all, >> How to output energies of

RE: [gmx-users] output energies by group

Dear all, >> How to output energies of different groups during the MD simulation? >with g_energy, if you have used energy groups in the simulation... No, I mean output the group energies in the flying ( using cut-off, during the simulation, not after the simulation), I think I have to modify the s

Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Dear Erik, I had the same problem as Arthur Roberts. So I downloaded your new version of gmx_system_xdr.h and gmx_system_xdr.c from http://bugzilla.gromacs.org/show_bug.cgi?id=55 Before I recompile gromacs, I checked the difference between your new version and the old one. The result is as follow

[gmx-users] pdb2gmx and ignh

Hello all, I am confused about what the -ignh option of pdb2gmx actually does. I have read the mailing list, the manual and many tutorials and short of browsing the source cannot find a definite answer. The man page claims that pdb2gmx will add hydrogens, however after using the ignh option to ign

RE: [gmx-users] problem with ambconv

Thanks, yes, that would be interesting as I plan on obtaining AMBER. Does it work with any version ? Diane -Original Message- From: [EMAIL PROTECTED] on behalf of David Mobley Sent: Fri 8/4/2006 3:00 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] problem with ambconv

Re: [gmx-users] problem with ambconv

Diane, We have an in-house script called amb2gmx written in collaboration with the Pande group that works for this purpose, although it requires an installation of AMBER. Let me know if you would like it. Thanks, David On 8/4/06, Diane Fournier <[EMAIL PROTECTED]> wrote: Hi I'm presently

[gmx-users] problem with ambconv

Title: problem with ambconv Hi I'm presently trying to use the ambconv program to convert amber topologies generated with antechamber v. 1.26 and tleap to gromacs format for use with the amber force field port. The problem is, I can't get the program to work. For example : $ ambconv -v -at

Re: [gmx-users] output energies by group

Mu Yuguang (Dr) wrote: Dear all, How to output energies of different groups during the MD simulation? with g_energy, if you have used energy groups in the simulation... Best regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://

Re: [gmx-users] trjconv problem

hi, similar happened to me, when i used the -b and -e flags of trjconv. to me it seemed that if you do not hit exactly the time frame as written in the trr file, trjconv will not output anything. when i used the -dump flag it worked, because then frames near the specified time are dumped. hope

[gmx-users] output energies by group

Dear all, How to output energies of different groups during the MD simulation? Best regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list

Re: [gmx-users] trjconv problem

Bjoern Windshuegel wrote: Hi everybody, I am trying to extract some frames from my md simulation using trjconv. For some frames this works fine but for others of the same simulation I get the following error message (for frame after 5590 picoseconds): Skipping frame500 time 5250.000 Se

[gmx-users] trjconv problem

Hi everybody, I am trying to extract some frames from my md simulation using trjconv. For some frames this works fine but for others of the same simulation I get the following error message (for frame after 5590 picoseconds): Skipping frame500 time 5250.000 Setting output precision to 0.00