[gmx-users] Unstable system [was: (no subject)]

[Padmani Sandhu]

I have also carried out MD simulation for the same comlex in water and that
worked perfectly.

On Thu, Oct 16, 2014 at 1:50 AM, 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%3Dcn7kjseE1qsZ3%252Fyd7n0%252FnivMrWPikx9abmED9c1Z42zTxtJsdJ4Nlq8B1dPjg96fP9AJ16aIbU8Kj7OnCGkj2WcFizgzmQOxfGDp41XzFi%252FbKCndwpcMOGrzAQcBkfgtR1XTfCbCQOE%253D%26key%3DO1Af6fqB%252BADty4CrThw297lFG47eK14mpIp97%252FGkvi0%253D&tc_serial=18958403331&tc_rand=66307849&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=18958403331&tc_rand=66307849&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>
>
>
>
> On 10/15/14 12:35 PM, Padmani Sandhu wrote:
>
>> Hello Justin,
>>
>>
>>
>> Epot = -3.4264112e+07
>> Fmax= 8.5767386e+02
>> from energy minimization.
>>
>>
> Seems reasonable.
>
>  I am using force field Gromos43a1 and ligand parameters were derived from
>> PRODRG.
>>
>
> PRODRG produces topologies full of errors.  Have you done any manual
> adjustments to improve the quality of the topology?
>
>  I have also minimized same protein-ligand complex in the water ealier.
>>
>>
> So minimization works, but does an MD simulation work?  That will help
> sort out whether or not the issue is related to the membrane.
>
> -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*