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

[Kavyashree M]

Sir,

     Yes sir I am using PME. And one more thing I noticed was, the protein
has
7 disulphide bonds, so when I reduce all the cystine to cysteine or to
alanine,
the the sum of charge group radii reduces from 0.31..nm to 0.30..nm and also
the
value of this is identical in case of alanine mutation or cysteine mutation.
    I finalised on the value of rlist = rcolomb = 1.35nm so as not to take
risk.
is that fine?

Thank you
M. Kavyashree

On Sat, Jan 22, 2011 at 6:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 <jalemkul at vt.edu<mailto:
>> 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
>>    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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