[gmx-users] charge group radii larger that rlist-rvdw
Kavyashree M
hmkvsri at gmail.com
Sun Jan 23 07:59:39 CET 2011
Dear gromacs users,
I went through the papers 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?
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),
Thank you
MKS
On Sat, Jan 22, 2011 at 11:18 PM, Justin A. Lemkul <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. 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>> 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>>> 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>>>> 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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>> -- ========================================
>>
>>
>> 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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> gmx-users mailing list gmx-users at gromacs.org
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