[gmx-users] problem in energy minimisation

[Justin A. Lemkul]

nitu sharma wrote:
> Dear Mark
> 
>         After doing second step of inflategro  i.e compression step  
> when I did the enery minimisation  with nstep-10000 in parameter file  
> it terminated after 1547 steps and written that -
> Converged to machine precision,
> but not to the requested precision Fmax < 2000
> 
> Double precision normally gives you higher accuracy.
> 
> writing lowest energy coordinates.
> 
> Steepest Descents converged to machine precision in 1547 steps,
> but did not reach the requested Fmax < 2000.
> Potential Energy  =  6.2109662e+05
> Maximum force     =  2.1254887e+04 on atom 6781
> Norm of force     =  7.1093488e+02
> 
> Can u suggest me probable solution of this problem .I am unable to 
> understand why this problem comes?
> 

You have clashes in your system.  Either the starting geometry of your protein 
is bad, or you have incorrectly applied InflateGRO and still have protein-lipid 
overlap.  Look at your output structure, see which atom corresponds to number 
6781, and see if you can tell where the problem is.

-Justin

> Thanks a lot
> Nitu Sharma
> Structural biology lab
> School of life Sciences
> Jawaherlal Nehru University
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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

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

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