Kavyashree M wrote:
Dear gromacs users,
I went through the papers dx.doi.org/10.1021/jp003919d
<http://dx.doi.org/10.1021/jp003919d>. on OPLS,
Its is stated in the paper
"Intermolecular interactions were truncated at 11 Å, with the standard
correction for the interactions beyond that radius. The electrostatic
interactions were quadratically feathered to zero over the last 0.5 Å
before the cutoff distance."
another OPLS reference
"Optimized Intermolecular Potential Functions for Liquid
Hydrocarbons" - J. Am. Chem. Soc. 1984, 106, 6638-6646
"In most cases, the intermolecular nonbonded interactions were truncated
at 11 Å 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."
So from these and other references of OPLS - AA force field, is it
possible to
set a range for vdw, coulomb interactions, so that we can use in that range
according to the system we are working on?
No. Only one value is possible.
Pardon me if the question is wrong. Your references and books will be of
great help for me.
Can anyone suggest regarding the preference of vdw_type (cutoff/shift or
switch),
I have seen both used in the literature. There is probably nothing wrong with a
plain cutoff for vdW, but you have to be able to justify your choices. Do some
more reading, find out if a plain cutoff for vdW is adequate, and make your
decision based on what you find.
-Justin
Thank you
MKS
On Sat, Jan 22, 2011 at 11:18 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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
<http://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>
<mailto: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>>
<mailto: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>>>
<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 <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>
<http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list
gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the
list.
Use the www
interface or send it to
gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>>.
Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
-- ========================================
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
========================================
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list.
Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>>.
Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
-- ========================================
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
========================================
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
