[gmx-users] Comparing the simulation

[rama david]

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 ??


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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