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 <jalem...@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
--
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University of Maryland, Baltimore
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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