Dear Amberites
I am trying to perform a gpcr membrane simulation using Amber8. My
system consists of: Protein, Ligand, Water, Lipids and Ions. My system
consists of ~ 63,000 atoms.
I have done minimization of the system stepwise: first minimizing only
water/ions, then water/ions and lipid, and then everything with
harmonic restraints on protein backbone (k = 50).
Now, I have to perform Equilibration of my system. I understand that
Eq. MD is usually done in 2 stages:
1. First raising the temp of the system to desired level (my case: 300
K) gradually using NVT ensemble (I understand that this step (NVT
equilibration before NPT equilibration) is very important to take care
of the voids that are created by deleting lipids etc. and spaces at
the edges of boundaries, which is especially true in my case).
Now, my question is of how long this initial NVT equilibration should
be CONSIDERING >>>>>
A. my system do have voids such as those created by deleting lipids
around GPCR in membrane, and also spaces at the edges as I have
manually defined the rectilinear box.
B. the large size of the gpcr-membrane system i.e. 63,000 atoms
QUESTION 1: I am thinking of some 300 PS to raise the temperature from
0 - 300 K using (600,000 steps with a time step of 2 using SHAKE). IS
THIS REASONABLE OR SHOULD THE LENGTH OF THIS NVT EQUILIBRATION BE MORE
OR LESS, AND HOW MUCH??
QUESTION2: After this NVT equilibration, what should be the
approximate length of NPT equilibration considering the above factors,
ballpark idea??
My NVT equilibration input file is described below >>>>>
------------------------------------------------------------------------------------------------------------------------
Angi Telmi in DMPC Water Ions: First 300ps NVT Equilibration MD with
harmonic rest on Protein backbone
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 60000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
restraint_wt=50.0
restraintmask=':1-297.CA,C,O,N,H'
/
------------------------------------------------------------------------------------------------------------------------
Thanks and I look forward to your suggestions.
Best Regards, -Akshay Patny (Olemiss)
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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 Jan 28 2007 - 06:07:49 PST
