[gmx-users] charge group radii larger that rlist-rvdw
Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 21 19:57:19 CET 2011
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
> Thanks
> MKS
>
> On Fri, Jan 21, 2011 at 5:20 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Kavyashree M wrote:
>
> Dear gromacs users,
>
> I am using gromacs 4.5.3, OPLSAA force field, and the cut
> off parameters
> are as shown below:
> ---------------------------------------------------------------------------------------------
> ;NEIGHBOURSEARCHING PARAMETERS
> nstlist = 10 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 = 1.36 ; CUT-OFF
> DISTANCE FOR SHORT RANGE NEIGHBOUR LIST
>
> ;ELECTROSTATICS
> coulombtype = PME ; METHOD FOR
> CALCULATING COULOMBIC INTERCATION - PME
> rcoulomb = 1.36 ; 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 ; WHEN TO START
> SWITCHING LJ POTENTIAL
> rvdw = 1.03 ; CUTOFF
> DISTANCE FOR LJ OR BUCKINGHAM INTERACTIONS
>
> ;EWALD
> fourierspacing = 0.12 ; GRID SPACING
> FOR FFT GRID FOR PME
> pme_order = 4 ; INTERPOLATION
> ORDER FOR PME
> ewald_rtol = 1e-5 ; RELATIVE
> STRENGTH OF EWALD SHIFTED DIRECT POTENTIAL
> optimize_fft = yes ; SAVES A FEW
> PERCENT FOR LONG SIMULATIONS
> -----------------------------------------------------------------------------------------------------
>
> For EM (energy minimisation) I initially had used
> rlist = rcolomb = 1.2; rvdw = 1.1; rvdw_switch = 1.0
> grompp gave the message:
> ##################
> Largest charge group radii for Van der Waals: 0.160, 0.157 nm
> Largest charge group radii for Coulomb: 0.168, 0.167 nm
>
> NOTE 1 [file md.mdp]:
> The sum of the two largest charge group radii (0.317) is larger
> than
> rlist (1.20000) - rvdw (1.10000)
> ##################
> So I changed the values to: rlist = rcolomb = 1.35; rvdw =
> 1.03; rvdw_switch = 1.0
> grompp message during em disappeared.
>
> During PR (position refinement), Again the message appeared for
> grompp
> ##################
> Largest charge group radii for Van der Waals: 0.168, 0.156 nm
> Largest charge group radii for Coulomb: 0.168, 0.164 nm
>
> NOTE 1 [file md.mdp]:
> The sum of the two largest charge group radii (0.324) is larger
> than
> rlist (1.35000) - rvdw (1.03000)
> ##################
> hence I changed the values to: rlist = rcolomb = 1.36; rvdw =
> 1.03; rvdw_switch = 1.0
> grompp message during pr disappeared.
>
> The same message repeated for MD
> ###################
> Largest charge group radii for Van der Waals: 0.171, 0.159 nm
> Largest charge group radii for Coulomb: 0.171, 0.166 nm
>
> NOTE 1 [file md.mdp]:
> The sum of the two largest charge group radii (0.330248) is
> larger than
> rlist (1.360000) - rvdw (1.030000)
> ###################
>
> My questions are:
> 1. Why does the charge group radii change in this way from em to
> pr to MD even though I
> am using same parameters
>
>
> Because EM changes coordinates, so the configurations of those
> charge groups probably changed.
>
>
> 2. What is the safest maximum value of rlist I can go up to? (is
> it 1.4nm according to "The Origin
> of Layer Structure Artifacts in Simulations of Liquid Water"-
> JCTC, 2006, 2, 1-11 paper?)
> 3. What is the minimum safest rvdw distance i can take?
>
>
> For #2 and #3, you should use settings that are recommended for the
> OPLS force field. Refer to the original literature for the force field.
>
>
> 4. According to the manual, when using switch they have
> suggested that ".. neighbor search
> cut-off rlist should be 0.1 to 0.3nm larger than rvdw..." then
> Why in the above case it goes
> more than 0.3nm?
>
>
> Usually over 0.3 nm is not necessary, but it seems in your case that
> you have some relatively large charge groups. This may or may not
> indicate something is wrong with your topology.
>
> The ad hoc changes you have made to the cutoffs to make a grompp
> message go away are probably not suitable. Refer to the OPLS papers
> for proper settings.
>
> -Justin
>
> Thanks in advance
> MKS
>
>
> --
> ========================================
>
> 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 at gromacs.org
> <mailto:gmx-users at 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-request at gromacs.org
> <mailto:gmx-users-request at 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
========================================
More information about the gromacs.org_gmx-users
mailing list