[gmx-users] Effect of time step size

[Justin Lemkul]

On 2/12/15 8:55 AM, Faezeh Pousaneh wrote:
> I see. thanks.
> Now can I continue simulations with the increased lincs values? or there is
> something wrong with my model and I should look for the source of
> unstability?
>

I would do the latter.  If conventional settings don't work for conventional 
applications, you're likely just fixing a symptom of something.

-Justin

> Best regards
> *Faezeh Pousaneh*
>
> On Thu, Feb 12, 2015 at 1:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/12/15 4:58 AM, Faezeh Pousaneh wrote:
>>
>>> Dear Justin,
>>>
>>> Thank you. Yes, both correspond to same setting except dt.
>>>
>>> No, expected value is not known.
>>>
>>> I have just tried to re-simulate with different values of lincs_itr and
>>> lincs_order (2 and 8 respectively) and I get similar values for densities.
>>> Could that be a good solution?
>>>
>>>
>> In principle, you shouldn't have to do that in situations like these (note
>> the descriptions of these options in the manual indicate only very specific
>> cases should require increasing them beyond default).  More likely, the
>> agreement after these changes indicates that there was something unstable
>> about the previous setup, such that the model is not producing reliable
>> physics when you increase dt too much.
>>
>>
>> -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

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