[gmx-users] Is it correct
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 23 16:04:36 CEST 2008
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 A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users