I am curious if there is some difference in the way an Equilibration Vs
Production molecular dynamics simulation should be setup in AMBER ?
I understand that output options such as NTWX, NTPR etc. should be adjusted
in Production MD. However, my concern is if certain options which affect
simulation should also be altered ???
>From one of the previous posts, I found that TAUP and GAMMA_LN was altered
the following way::
Equilibration Run:
TAUP = 2.0
GAMMA_LN = 1.0
Production Run:
TAUP = 1.0
GAMMA_LN = 5.0
Does this make sense, I will be glad if you have any suggestions on this
issue?
Also, is it a good idea to use IWRAP = 1 or post-processing using ptraj (for
centering images) is better??
Here is one of my equilibration MD file which I used::
------------------------------------------------
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2,
ntp = 2,
pres0 = 1.0,
taup = 2.0,
cut = 10,
ntr = 0,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 25000, dt = 0.002,
ntpr = 100, ntwx = 2000, ntwr = 1000
------------------------------------------------
I look forward to your suggestions.
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 Mar 04 2007 - 06:07:14 PST
