[gmx-users] Semiisotropic pressure coupling

[shivangi nangia]

Dear Justin,

I have sent the files to you at your vt.edu


Thanks,

sxn

On Sun, Feb 15, 2015 at 7:59 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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> Gromacs Users mailing list
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