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.
From the generated energy file one optionally could select not only coulomb and
vdw terms between the goups lipid1, lipid2 and lipid3 but also between lipid1
and lipid1. The coulomb output of lipid1-lipid1 is 0 while vdw is ~ -30-40
kJ/mol. Since the latter is the vdw energy of a lipid with itself should one
understand this value as the interaction between different atoms of one lipid?
Yes. There are several intramolecular terms that can come into play here.
The vdw interactions between lipid1-lipid2 is also ~ -30-40 kJ/mol. Apart from
the feeling that these vdw numbers are ~ twice larger than they should does
this procedure contain some obvious problems?
Upon what do you base your feeling? In principle, this is a very simple
calculation to decompose the short-range nonbonded interactions in a pairwise
fashion. Note that these are not free energies and there is no reason to
believe that any given force field will be able to produce a physically
meaningful value here as the force field almost certainly wasn't parameterized
to reproduce such a value.
-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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