[gmx-users] charge group radii larger that rlist-rvdw
Justin A. Lemkul
jalemkul at vt.edu
Sat Jan 22 13:56:16 CET 2011
Kavyashree M wrote:
> 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
> 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
You're using PME. In the first paragraph of the introduction, it is stated that
the spurious effect does not occur with PME.
> Thanking you
> M. Kavyashree
> On Sat, Jan 22, 2011 at 12:27 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> Kavyashree M wrote:
> 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
> 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.
> 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 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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