[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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