[gmx-users] charge group radii larger that rlist-rvdw
Justin A. Lemkul
jalemkul at vt.edu
Sun Jan 23 14:10:03 CET 2011
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto: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>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto: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>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto: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> <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> <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> <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
>
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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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