shahrbanoo karbalaee wrote:
Dear justin
In my work MD peptide(with 13 aa) I use this md.mdp.would ypu please
say me Is that correct.
The definition of "correct" is up to you. I'll give you a few pointers
(embedded below), but the leg-work of determining the validity of the parameters
is your homework, not mine (or anyone else's!)
title = cpeptide MD
cpp = /lib/cpp
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5000 ; total 5 ps.
nstcomm = 1
nstxout = 50
nstvout = 0
Are you sure you don't want to save velocities every now and again? If your run
crashes because of a hardware problem, you may want to be able to restart it...
What about using nstxtcout? The output file will be greatly compressed relative
to the .trr. It will save a lot of disk space when running analysis.
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
All of the parameters from nstlist to rvdw have values that are generally
determined by the force field and its derivation scheme. Check the literature.
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = protein sol
ref_t = 300 300
As long as you have no ions this is fine.
; Pressure coupling is not on
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
As long as you are expecting an NVT ensemble, this is also fine.
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
Is this .mdp file for equilibration or production? You refer to it as the
md.mdp, but if you're re-generating velocities, I certainly hope this .mdp file
is for the beginning of equilibration. If you re-generate velocities
repeatedly, then you don't get a continuous trajectory.
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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