[gmx-users] Re: Ligand is moving far away after energy minimization

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 5 13:07:56 CET 2009

Ms. Aswathy S wrote:
> Ms. Aswathy S wrote:
>> Dear Gromacs users,
>> I am doing the MD of protein ligand complex. When I did the energy minimization of this complex,   in the result , the ligand molceule is moving far away from the protein.
>> What could be the possible reason? can anyone tell me how can i overcome this?
> Two possibilities come to my mind.
> 1. The parameters of the ligand are inappropriate, causing the ligand to be 
> ejected from the active site.  This is unlikely in a simple EM procedure, and 
> probably would cause lots of LINCS or "blowing up" warnings.
> 2. More likely: Your protein is positioned near a box edge and the ligand is 
> crossing periodic boundaries.  Consider how you set up the box and read about PBC:
> http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
> -Justin
> Here I dint get any error message as you mentoined in th first possiblity.Then about the seocnd suggestion, only two options provided to in the manual. pbd : no and pbc: xyz. I havn;t found any change in my problrm.
> can you rxplain a liitle bit more. waiting for you reply....

Given the information you've provided, no.  If you can post the following 
information, maybe things will be more clear on our end:

1. The *exact* commands given to set up your system
2. The contents of your .mdp file


>> Thanks in advance.
>> Aswathy
>> Amrita School of biotechnology
>> Dept. Biotechnology
>> Ext. 3108
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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