[gmx-users] Re: Poteintial energy of my system

shika pqah123 at gmail.com
Wed Dec 12 09:10:05 CET 2012

Dear Shima,

I also got the same problem..The value of the potential energy should
be in negative value..Maybe you can increase the steps?

Or it might be the system that you do is something wrong

On Wed, Dec 12, 2012 at 3:32 PM, Shima Arasteh [via GROMACS]
<ml-node+s5086n5003681h95 at n6.nabble.com> wrote:
>  Dear users,
> I ran grompp on my system:
> #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
> #mdrun -deffnm em
> When I get the ouput, the potential energy is a positive integer, I think it
> doesn't seem sensible. Does it?
> Steepest Descents converged to Fmax < 100 in 4998 steps
> Potential Energy  =  1.1410846e+04
> Maximum force     =  9.4570084e+01 on atom 8800
> Norm of force     =  3.2672191e+00
> What do you suggest me about my system? Do you think that it has any
> problem?
> Sincerely,
> Shima
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Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
alternative email : syafiqahabdulghani at gmail.com

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