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 <jalem...@vt.edu
<mailto:jalem...@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
========================================
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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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