Hi Jena,
The initial velocities are generated as a Boltzmann distribution of
velocities based on the initial temperature you set (tempi). Of course if
this is a restart then this step is skipped and they are instead read from
the restart file.
You can obtain a different Boltzmann weighted set of velocities by changing
the random see. Set IG=xxxxxx in the &cntrl namelist to a value of your
choice.
If however, you want to manually set the initial velocities then this is
more complicated. You would need to take a restart file and manually change
the velocities for each atom. This would likely need to be scripted since it
will be very tedious by hand.
If you really believe that it is the initial velocities causing the problems
then you might be better setting tempi=0.0 and heating slowly with a
thermostat using NMR restraints to control the value of temp0.
Good luck,
Ross
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|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- <mailto:ross.rosswalker.co.uk>
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Jena M
Sent: Tuesday, May 13, 2008 9:38 AM
To: amber.scripps.edu
Subject: AMBER: initial velocities of MD
Hi,
I have run a MD simulation of a protein and the trajectory revealed
instabilities in some regions of that protein. So I would like to ran the MD
simulation again but using different initial velocities, in order to see if
I these instabilities are kept. Does anyone know how to change the initial
velocities? Can I use the same top and crd files to initiate the
equilibration phase?
Thanks a lot,
Jena
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Received on Wed May 14 2008 - 06:07:45 PDT
