On 2/19/13 1:36 AM, Anu Chandran wrote:
Sir,
Thank you for the reply. As per the suggestion, I tried increasing the
rlist. Note or warning stopped when rlist was increased to 1.8. Also with
this value of rcoulomb, the box size also needs to be increased. I would
like to know whether it is fine to keep rlist 1.8 and also whether there is
any other alternative rather than increasing rlist since increase in rlist
requires an increase in box size.
I would investigate why you have such large charge groups. For a protein in
water (which is what you appear to have based on the .mdp file), you should not
have such large charge groups. Haphazardly adjusting cutoffs can have a
negative effect on the simulation. Increasing rlist may result in poorer
performance. Why are you using a switching potential for van der Waals
interactions? Exact specifications for OPLS are hard to come by in the
literature, but most commonly one sees:
rvdw = 1.0
vdwtype = cutoff
rlist = 1.0
rcoulomb = 1.0
coulombtype = PME
-Justin
Thank you,
with regards
Anu
On Fri, Feb 15, 2013 at 5:28 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote:
I am tyring to do a simulation of a monomer and an octamer of the same
molecule
using gromacs 4.5.3 with opls force field. Monomer simulations ran with
out
any note or
warning, but when i tried to do nvt equilibration for the octamer, i got
the
following note while running grompp
"NOTE 1 [file nvt.mdp]:
The sum of the two largest charge group radii (0.779095) is larger than
rlist (1.400000) - rvdw (1.000000)"
The mdp file used is as follows:
define = -DPOSRES
integrator = md
dt = 0.002
nsteps = 50000
nstcomm = 10
nstxout = 100
nstvout = 100
nstlog = 100
nstenergy = 100
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = PME
rcoulomb = 1.4
epsilon_r = 1
vdwtype = Switch
rvdw_switch = 0.9
rvdw = 1.00
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
Tcoupl = nose_hoover
tc_grps = Protein Non-Protein
tau_t = 0.4 0.4
ref_t = 300 300
nh-chain-length = 1
pcoupl = no
gen_vel = yes
gen_temp = 300.0
gen_seed = 1984
continuation = no
constraints = all-bonds
constraint-algorithm = LINCS
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
Can anybody please help me on how to go about with it?
1) Increase RLIST
2) Re-distribute atoms among charge groups so that to make charge
groups [spatially] smaller.
Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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