[gmx-users] Effect of time step size

[Faezeh Pousaneh]

Thanks a lot Justin!


Best regards


On Fri, Feb 13, 2015 at 2:32 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

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