Kavyashree M wrote:
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.
That is an older version of OPLS. See dx.doi.org/10.1021/jp003919d. The
cutoffs are much clearer.
-Justin
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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto: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> <http://vt.edu>
<http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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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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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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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