On 7/23/13 1:54 PM, Davit Hakobyan wrote:
Thank you very much for your continuous support.
Date: Tue, 23 Jul 2013 12:06:57 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Calculate interaction energy dynamically
On 7/23/13 11:05 AM, Davit Hakobyan wrote:
Thanks so much for the suggestion.
By using the command:
trjorder -f system.trr -s system.tpr -n system.ndx -da 3 -na 12 -r 2.0 -o
system_ordered.trr
the resulting system_ordered.trr indeed contained lipids 2,3,4... in the
closest proximity to lipid 1 (within the specified cuttoff of 2.0 nm).
Then by specifying new energy groups like lipid1, lipid2, etc the energy file was
generated with the "rerun" flag:
mdrun_-s system_ordered.tpr -rerun system_ordered.trr -o
system_ordered_useless.trr -c system_ordered.gro -e system_ordered.edr
many warnings were shown like:
WARNING: there may be something wrong with energy file system_ordered.edr
Found: step=-1, nre=68, nblock=0, time=31000.
Trying to skip frame expect a crash though
WARNING: there may be something wrong with energy file system_ordered.edr
Found: step=-1, nre=68, nblock=0, time=32000.
Trying to skip frame expect a crash though
WARNING: there may be something wrong with energy file system_ordered.edr
Found: step=-1, nre=68, nblock=0, time=33000.
Trying to skip frame expect a crash though
Do these warnings point to some error?
Where do they come from - mdrun? g_energy? gmxcheck? If you haven't run
gmxcheck on the .edr file, please do.
The above warnings are issued by mdrun. The g_energy generates similar warnings
like:
WARNING: there may be something wrong with energy file system_ordered.edr
Found: step=-1, nre=68, nblock=0, time=74000.
Trying to skip frame expect a crash though
WARNING: there may be something wrong with energy file system_ordered.edr
Found: step=-1, nre=68, nblock=0, time=75000.
Trying to skip frame expect a crash though
Last energy frame read 75 time 75000.000
...
The gmxcheck command:
gmxcheck -f system_ordered.trr -c system_ordered.tpr -n system_ordered.ndx -e
system_ordered.edr
does not give any warning/error.
Can you please provide the actual gmxcheck output?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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