[gmx-users] hi

[Justin A. Lemkul]

Please choose an informative subject line, as it will help attract the attention 
of someone interested in helping you.

PAVAN RELISH DESTINY RESOLVING CRUX OF LIFE......... wrote:
>              I am new to Gromacs & using it with Amber force field amber03,
>              i am able 2 run my system of DNA till steepest descent but 
> when i tried to run it for cg it showed 
>              that can not work with so much of  constrains so i tried to 
> run it with -Dposres          

Minimization with position restraints serves very little, if any, purpose in my 
mind.

>              directly to mdrun with md integrator it showed an error 
> message "wrote pdb files with previous & current 
>              co-ordinate segmentation fault." 
>                                                          how can i 
> modify my mdp file to overcome this problem ?

Your system is insufficiently minimized and/or equilibrated.  Please see the 
following:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation

-Justin

-- 
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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

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