[gmx-users] Semiisotropic pressure coupling

[shivangi nangia]

Hello Justin,

I ran the simulation for 100 ns and I still get low APL at 303 K, 0.58 nm^2
 :(

Thanks in advance.
sxn





On Fri, Feb 13, 2015 at 5:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/13/15 5:00 PM, shivangi nangia wrote:
>
>> Hello All,
>>
>> Thank you all for you input.
>>
>> I now have access to GROMACS 5.0.
>>
>> On using the recommended settings, the APL is sill dropping within 3 ns of
>> the simulation.
>>
>
> 3 ns is orders of magnitude too short to draw any conclusions.  Simulate
> out to 100 ns and we'll talk :)  I only say this because I know the APL can
> be reproduced with the settings I gave in CHARMM and GROMACS with very
> close agreement.
>
> <snip>
>
>  nstlist                  = 1
>>
>
> Yikes!  You're losing a ton of performance here (though check the log to
> make sure Verlet adjusted this to something more suitable).  Setting
> nstlist = 1 is only for energy minimization.
>
>
> -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.
>