[gmx-users] Semiisotropic pressure coupling

[Justin Lemkul]

On 2/14/15 9:52 PM, shivangi nangia wrote:
> Hello Justin,
>
> I ran the simulation for 100 ns and I still get low APL at 303 K, 0.58 nm^2
>   :(
>

That outcome is inconsistent with everything I have seen from our own internal 
testing and published works that use GROMACS.  Something else must be up.  If 
you post all of your input files somewhere that I can download them, I'll try to 
take a look.

-Justin

> 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
>>
>> ==================================================
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-- 
==================================================

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

==================================================