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

[Shima Arasteh]

What are the possible solutions to solve the problem? 

My system is composed of protein, POPC, ions, and water. I follow the approached suggested in kalp15-DPPC tutorial.
And I got such an incorrect potential for the first grompp.
Would you please guide me?

I would appreciate ur suggestions.

Sincerely,
Shima


----- Original Message -----
From: shika <pqah123 at gmail.com>
To: gmx-users at gromacs.org
Cc: 
Sent: Wednesday, December 12, 2012 11:40 AM
Subject: [gmx-users] Re: Poteintial energy of my system

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,
Selangor.
013-7188131
alternative email : syafiqahabdulghani at gmail.com




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