[gmx-users] electrostatic interactions

[Justin A. Lemkul]

abdullah ahmed wrote:
> Thank you for your reply,
> 
> Settings:
> I am using the procedure outline by the "speptide" tutorial (i.e. 
> pdb2gmx, followed by editconf, genbox, grompp, and mdrun). The ".mdp" 
> file I've used is as follows:
> 
> ;    User spoel (236)
> ;    Wed Nov  3 17:12:44 1993
> ;    Input file
> ;
> cpp                 =  /usr/bin/cpp
> define              =  -DPOSRES
> constraints         =  none
> integrator          =  steep
> nsteps              =  100
> ;
> ;    Energy minimizing stuff
> ;
> emtol               =  20
> emstep              =  0.01
> 
> nstcgsteep          =  10
> nstcomm             =  1
> ns_type             =  grid
> rlist               =  1
> rcoulomb            =  1.0
> rvdw                =  1.0
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
> coulombtype         = PME
> 
> Force field: Encad all atom force field, using full sovent charges.
> 
> Local geometry is identical with the exception of the second charged 
> residue, which is replaced by Leucine in one structure. 
> 

Well, all you've done is a simple, restrained energy minimization, which won't 
tell you much about anything.  I don't see much point in using restraints during 
EM anyway.  Running real, unrestrained MD and obtaining suitable averages for 
energies is the only way to make the conclusions I think you're after.

-Justin

> 
> 
> ------------------------------------------------------------------------
> Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up 
> now. <https://signup.live.com/signup.aspx?id=60969>

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================