(unknown charset) Re: AMBER: Difference in Equilibration & Production MD in Amber

From: (unknown charset) Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Wed, 28 Feb 2007 15:54:13 -0500

Akshay Patny wrote:
> 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?
IMHO, that seems a bad idea. If you change the thermostat parameters, or
any other parameter that influences the system, you should let the
system relax before doing any kind of "production" run. (You may get
away with that though, if the new parameters are close enough to the old
> Also, is it a good idea to use IWRAP = 1 or post-processing using ptraj (for
> centering images) is better??
This depends on what you are doing. For long simulation, unless you are
using binary trajectories, the numbers can get too large for the field
size and mess with the trajectory file, unless you are using IWRAP=1.
However, that can also be a problem depending on the properties you are
interested in...

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Received on Sun Mar 04 2007 - 06:07:14 PST
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