[gmx-users] energy minimization

[Justin A. Lemkul]

subarna thakur wrote:
> Hello
> Can increase the emtol from 1000 to 10000 KJ mol ^- 1 nm^-1?

I wouldn't recommend it.  That would be a really large maximum force, which 
would probably cause your system to be very unstable.  Look at your original 
structure to see what might be wrong instead of just trying to find a way to 
push forward.

-Justin

> ^ 
> ^subarna
> 
> ------------------------------------------------------------------------
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Thu, 10 December, 2009 2:33:23 PM
> *Subject:* Re: [gmx-users] energy minimization
> 
> subarna thakur wrote:
>  > I am doing the energy minimization of a protein using the following 
> keywords in em.mdp file-
>  > cpp                =  /usr/bin/cpp
>  > define              =  -DFLEX_SPC
>  > constraints        =  none
>  > integrator          =  steep
>  > nsteps              =  3000
>  > ;
>  > ;    Energy minimizing stuff
>  > ;
>  > emtol              =  1000
>  > emstep              =  0.01
>  >
>  > nstcomm            =  1
>  > ns_type            =  grid
>  > rlist              =  1
>  > coulombtype        =  PME
>  > rcoulomb            =  1.0
>  > rvdw                =  1.0
>  > Tcoupl              =  no
>  > Pcoupl              =  no
>  > gen_vel            =  no
>  >
>  > -----------------------------------------------------------------
>  > I am getting the ouput as following---------
>  > Steepest Descents converged to machine precision in 67 steps,
>  > but did not reach the requested Fmax < 1000.
>  > Potential Energy  = -4.0967048e+06
>  > Maximum force    =  3.7720719e+04 on atom 5530
>  > Norm of force    =  1.7014005e+02
>  > -----------------------------
>  > Can anybody suggest what changes I can make
> 
> Well you can play with the EM step size, or see if atom 5530 looks 
> unhappy, or you can move on to your equilibration and hope nothing's 
> seriously wrong.
> 
> Mark
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-- 
========================================

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

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