[gmx-users] Comparing the simulation

[Justin Lemkul]

On 7/20/13 9:12 AM, rama david wrote:
> Dear Justin,
> Thank you for your Prompt Reply.
>
>     I run a at least 4-5 run of each peptide.
> The result are like the xx peptide form beta structure early than yy
> peptide in each run.
> I just used the different tau_P ( relaxation time ) for NPT and MD
> production run.
> XX tau_p = 2                   YY tau_p= 1
>
>
> NVT parameter are same.
>
> On these basis can I make the interpretation that XX form beta sheet
> structure early than YY
> though they uses the same barostat but different tau_P ??
>

I've already expressed by opinion on that in the previous post.

-Justin

>
> With Best Wishes and Regards,
> Rama David
>
>
>
>
> On Sat, Jul 20, 2013 at 4:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/20/13 5:27 AM, rama david wrote:
>>
>>> Dear Friends,
>>>                        I did the Simulation study for self
>>> assembly of peptides . ( I used G96 53a6 FF )
>>>
>>> In First Experiment, I put the two XX peptide far from each other 2.0 nm,
>>>    and run the simulation.
>>> In the second experiment I put the two YY peptide seperated by 2.0 nm.
>>> and run the simulation.
>>>     In nvt I used the sane parameter, but In NPT, MD simulation I run
>>> the Parrinello-Rahman barostat with tau_P 2.0 ns for XX peptide and tau_P
>>> 1
>>> for
>>> YY peptide.
>>>     I found that peptide YY interaction start at 80ns and XX interaction
>>> start at 10 ns.
>>>
>>>
>>>      I have following Question.
>>>    1>.        Is it possible to compare  two MD simulation which used the
>>> same barostat   but having the different tau_P ( Relaxation time).
>>>
>>>
>> You'll have to examine pressure distributions very carefully, but I am
>> inherently suspicious of trying to salvage results that were based on a
>> mistake.
>>
>>
>>   2>.         Could I make the interpretation that  XX peptide start
>>> interact
>>> more early   than YY ??
>>>
>>>
>> Based on one simulation of each?  No.
>>
>>
>>   3>>. Would we compare  the result between the simulation that uses the
>>> different barostat ant thermostat but still using the same Force field.
>>>
>>>
>> If you are altering both thermostat and barostat, I would be extremely
>> skeptical of the results.  Apply consistent methods.
>>
>> -Justin
>>
>> --
>> ==============================**====================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
>> (410) 706-7441
>>
>> ==============================**====================
>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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