# (unknown charset) AMBER: Density of a system in MD

From: (unknown charset) Akshay Patny <akshay17.olemiss.edu>
Date: Thu, 15 Feb 2007 14:45:27 -0600

Dear Amber users

I am simulating a GPCR in DMPC membrane using Amber 8. My system consists of
62,000 atoms >>>

1. Protein
2. Ligand
3. Water (intracellular/extracellular)
4. Lipids (DMPC bilayer)
5. Ions

After minimization, I have performed 100ps NVT to raise temp from 0-300K and
then I am performing constant pressure 200 ps NPT simulation of this system
at 300K.

Can anybody suggest that what should be the approximate density of such a
system. The density of water at 300K is approx. 1.0 g/cm^3. So, I am
guessing for such a system the density will be much above that value??
----------------------------------------------------------------------------
-------------------
During the initial 200 ps NPT simulation of the system >>>
Following were the values of Volume and Density >>>>

Start ---- 0.2 ps
VOLUME = 1261363.3851
Density = 0.4953

Now ----- my system has reached upto 92 ps yet
VOLUME = 1058401.9254
Density = 0.5903
----------------------------------------------------------------------------
-------------------

So, I can say that the volume is constantly decreasing and the density is
increasing for my system. So shall I equilibrate this system until both
values becomes approximately constant?? My question is what will be the
approx density value which I should be looking at for such a system??

I will really appreciate if people with experience in membrane protein

Thanks a lot, Best Regards

Akshay

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Akshay Patny
PhD Candidate (5th Yr.), Computational Chemistry
Department of Medicinal Chemistry, School of Pharmacy
The University of Mississippi
805 College Hill Rd, # 9, Oxford, MS 38655
E-mail: akshay17.olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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Received on Sun Feb 18 2007 - 06:07:24 PST
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