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.

---------------------------------------------------------------------------------
; 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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