Kavyashree M wrote:
Sir,
System is a protein with 123 aa. No modifications were made on the
pdb file,
and it was submitted to pdb2gmx by removing all HETATMs, retaining only
protein
atoms. topology was created entirely by pdb2gmx and no other molecule
was introduced.
I will go through the OPLSAA paper, but if I increase rlist to
1.4nm without reducing
rvdw according to "The Origin of Layer Structure Artifacts in
Simulations of Liquid Water"
- JCTC, 2006, 2, 1-11, will it not cause orderedwater shell during
simultion?
You're using PME. In the first paragraph of the introduction, it is stated that
the spurious effect does not occur with PME.
-Justin
Thanking you
M. Kavyashree
On Sat, Jan 22, 2011 at 12:27 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Kavyashree M wrote:
Sir,
What exactly can be wrong with the topology? As I tried with
I don't know, what's in your system? Was the topology created
entirely by pdb2gmx, or have you introduced some other molecules
that you've parameterized?
different PDBs of same structure at higher resolutions too, I am
getting
almost similar charge group radii, so can you kindly elaborate about
what can go wrong in the topology to get such values?
Large charge groups indicate that a fair number of atoms have been
included in the same charge group. Usually only two or three atoms
are in a charge group, rendering them fairly small. With PME, the
effects may not be that large, i.e.
http://lists.gromacs.org/pipermail/gmx-users/2010-November/056219.html,
but it's still worth investigating what your largest charge group is
that's causing this problem. If the topology is sound and is based
entirely upon standard force field files, it may suffice to simply
increase rlist to 1.4 nm, leaving all the other cutoffs at 1.0,
which I believe is standard for OPLS (but don't just take my word
for it).
-Justin
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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