[gmx-users] charge group radii larger that rlist-rvdw
Kavyashree M
hmkvsri at gmail.com
Sat Jan 22 17:45:02 CET 2011
I went through few papers related to OPLS-AA, but could not find
any specific values mentioned for vdw and coulomb intecations..
In one of the papers
".....In most cases, the intermolecular nonbonded interactions were
truncated at 11Å based on roughly the center-of-mass separations
with quadratic smoothing of the interaction energy to zero over the
last 0.5 Å. The cutoff for alkenes and acetals was 13 Å, while for
propanol, cyclohexane, 2-methyl-2-propanol, phenol, ethyl methyl
sulfide, NMA, DMA, and NMP it was extended to 15 Å....."
J. Am. Chem. Soc. 1996, 118, 11225-11236.
So does this cut off refer to coulombic interactions?
is it correct if iI use the following parameters for OPLS-AA force field?
-----------------------------------------------------------------------------
;NEIGHBOUR SEARCHING
nstlist = 10 ; FREQUENCY WITH WHICH NEIGHBOURLIST
IS UPDATED
ns_type = grid ; TYPE OF NEIGHBOUR SEARCH GRID OR
SIMPLE
pbc = xyz ; DIRECTION OF PERIODIC BOUNDARY
CONDITIONS USAGE
rlist = 1.4 ; CUT-OFF DISTANCE FOR SHORT RANGE
NEIGHBOUR LIST
;ELECTROSTATICS
coulombtype = PME ; METHOD FOR CALCULATING COULOMIC
INTERCATION - PARTICLE MESH EWALD
rcoulomb = 1.4 ; CUTOFF DISTANCE FOR ELECTROSTATIC
INTERACTIONS
epsilon_r = 1 ; RELATIVE DIELECTRIC CONSTANT
;VAN DER WAALS
vdwtype = Switch ; METHOD FOR TREATING VANDERWAAL'S
FORCES
rvdw_switch = 0.9
rvdw = 1.00 ; CUTOFF DISTANCE FOR LJ OR
BUCKINGHAM INTERACTIONS
--------------------------------------------------------------------------------------------------------------------
Thanks
MKS
On Sat, Jan 22, 2011 at 6:41 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Kavyashree M wrote:
>
>> 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?
>>
>>
>
> As I said before, read the OPLS paper. 1.35 nm does not sound right.
>
> -Justin
>
> Thank you
>> M. Kavyashree
>>
>>
>> On Sat, Jan 22, 2011 at 6:26 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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>
>> <mailto: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> <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 <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
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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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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