On 1/24/13 10:26 AM, Raghuvir R. S. Pissurlenkar wrote:
Hi
I have tried to write a grompp.mdp file for simulated annealing of a peptide
(~30 aa) in implicit solvent.
Please someone could tell me if the parameters set are fine for the same.
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; Preprocessing
define = -DFLEXIBLE
Irrelevant if there is no explicit water, and shouldn't be used for MD anyway
(only EM).
; Run control
integrator = md
dt = 0.002
nsteps = 500000; 1 ns
comm-mode = angular
nstcomm = 1000
grompp will complain about this. nstcomm should be equal to nstcalcenergy.
comm-grps = system
; Langevin dynamics
bd-fric = 0
ld-seed = 1993
; Output control
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
; Neighbor searching
cutoff-scheme = group
nstlist = 10
Better to use a fixed neighbor list (nstlist = 0) to use the all-vs-all kernels.
You're using infinite cutoffs anyway, so all interactions are calculated.
There's no point in updating a neighbor list that contains every atom in it.
ns-type = simple
pbc = no
rlist = 0
; Electrostatics
coulombtype = cut-off
rcoulomb = 0
; VdW
vdwtype = cut-off
rvdw = 0
; Temperature coupling
tcoupl = v-rescale
tc-grps = Protein
tau-t = 0.5
ref-t = 300.0
; Pressure coupling
pcoupl = no
; Simulated annealing
annealing = single
annealing-npoints = 1
annealing-npoints = 0 10 20 30 40 50
You've got the same keyword twice. The first instance (annealing-npoints = 1)
is correct; there is only one group specified in tc-grps.
Presumably what you want here is annealing-time rather than annealing-npoints.
annealing-temp = 300 320 340 360 380 400
Simulated annealing is a linear increase in temperature, and thus all you need
to do to warm from 300K to 400K over 50 ps is:
annealing-time = 0 50
annealing-temp = 300 400
; Velocity generation
gen-vel = yes
gen-temp = 300.0
gen-seed = 173529
; Bonds
constraints = all-bonds
constraint-algorithm = P-LINCS
P-LINCS is not a valid setting. If running in parallel, LINCS automatically
uses P-LINCS.
lincs-order = 4
lincs-iter = 1
; Implicit solvent
implicit-solvent = GBSA
gb-algorithm = OBC
nstgbradii = 1.0
rgbradii = 1.0
Set both nstgbradii and rgbradii to zero when using infinite cutoffs.
-Justin
--
========================================
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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