[gmx-users] Effect of time step size

[Faezeh Pousaneh]

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?

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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