[gmx-users] Problem in equilibration of POPS lipid bilayer

Padmani Sandhu padmanisandhu09 at gmail.com
Thu Jul 9 05:52:44 CEST 2015


Thank you Justin, I was not paying attention toward the wrong .itp file. I
found correct topology of POPS from the site of "*Robert Vácha*" (
http://lcc.ncbr.muni.cz/~robert/publikacee.htm) and now the problem is
sorted.






With regards,


Padmani




On Wed, Jul 8, 2015 at 5:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

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> On 7/8/15 7:57 AM, Padmani Sandhu wrote:
>
>> Hello all,
>>
>>
>>
>> I have generated a mixed lipid bilayer constituting POPS and POPC lipid
>> molecules. I am trying to perform MD simulation but the POPS lipid
>> molecules are tearing apart on energy minimization.
>>
>>
> So either your coordinates are bad, the topology has a problem, your .mdp
> settings are wrong, or whatever means you've prepared the system is
> inadequate.  Unfortunately you've provided no useful information, so it's
> pointless to guess.
>
> Refer to http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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-- 
*Padmani sandhu*
*Research Scholar,*
*Center for Computational Biology and Bioinformatics,*
*Central University of Himachal Pradesh,*
*Temporary Academic Block, Shahpur *
*Pin 176206, District Kangra,*
*Himachal Pradesh, India*


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