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

[Padmani Sandhu]

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:

>  [image: Boxbe] <https://www.boxbe.com/overview> This message is eligible
> for Automatic Cleanup! (jalemkul at vt.edu) Add cleanup rule
> <https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3DmmoH72dBff9ZLiT0LvtDttmTeoAIJHUudSk%252F0Jy3Wj5PDtaYCmYNUvLiwcpVGQetXmORmmUwTKY1iZgmS3u%252BT1Cuf1zNqR0VTjA6SCIvYvhvQHqzA0fRA5DYa%252BEDp%252Bnzaw0RjafgFxM%253D%26key%3DE%252F3a6xm5v2zwgzdAiaRFYXkYDnPFgp7boBDAfYepou8%253D&tc_serial=21904080572&tc_rand=1921652829&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>
> | More info
> <http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=21904080572&tc_rand=1921652829&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>
>
>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>


-- 
*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*