[gmx-users] charge group radii larger that rlist-rvdw

Kavyashree M hmkvsri at gmail.com
Sat Jan 22 05:21:22 CET 2011


     System is a protein with 123 aa. No modifications were made on the pdb
and it was submitted to pdb2gmx by removing all HETATMs, retaining only
atoms. topology was created entirely by pdb2gmx and no other molecule was

     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

Thanking you
M. Kavyashree

On Sat, Jan 22, 2011 at 12:27 AM, Justin A. Lemkul <jalemkul at 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
> 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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