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
Dear all,
How to output energies of different groups during the MD simulation?
Best regards
Yuguang
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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.
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
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
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
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
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
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