[gmx-users] Is it correct

[Justin A. Lemkul]

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


--
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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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