[gmx-users] bad contacts on lipid tails

[Mohsen Ramezanpour]

Hi Justin,

I could solve the problem.
Recognizing the lipids which had overlap and subsequent removal of one of
them in each pair could solve it.
Now, it can be run with a time step of 2 without any problem.

Cheers,
Mohsen

On Wed, Jun 14, 2017 at 3:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/14/17 5:23 PM, Mohsen Ramezanpour wrote:
>
>> I have done equilibration for almost 45 ns or even 60 ns for one test
>> system.
>>
>> I expected with this energy and this equilibration time, it works fine.
>> But
>> it fails.
>>
>> I will construct the systems as you suggested to see what I get.
>>
>>
> With such a long equilibration, there's no reason it should fail with dt =
> 2 fs if the clashes have been eliminated, because I would expect they
> should be gone after a few ps.  I'd suspect something else in the topology
> or .mdp file but you'll have to do a more thorough diagnosis (e.g.
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
> Diagnosing_an_Unstable_System)
>
>
> -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.
>



-- 
*Rewards work better than punishment ...*