Dear Li,
> I'm trying to simulate a molecule in vacuum using amber for
> comparison. But
> it always goes beyond the virtual box. For some reason, I
> don't want to rm
> the translational and rotational motion of center-of-mass too often.
> In that case, what can I do then? PS: Is there a way for me
> to set the size
> of the virtual box?
If you are using ntt=1 for temperature control, or no thermostat, you only
need to remove center-of-mass motion once at the beginning. After this any
centre of mass motion that the system gains will be due to round off error
and be minimal.
An easy way of doing this is to run an initial run of only 100 steps with
nscm=50. Then use the restart file generated from this short run as the
starting structure and velocities for your main run. Make sure you set
irest=1 and ntx=5.
This will get you around the problem of the molecule diffusing out of the
box due to centre of mass motion it gains from the initial velocity
distribution.
As for setting the size of the virtual box I'm not sure if this is possible,
ultimately the limitation should be removed all together for vacuum
simulations but this is something for later versions. For the moment you
could always setup a periodic box (add the box dimensions and 3 angles to
the end of the inpcrd file) that is large. Then you can run a constant
volume periodic boundary simulation and as long as cut is less than half the
box length and you have pme turned off you will get the same results as gas
phase.
I hope this helps
All the best
Ross
/\
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Wed Aug 24 2005 - 05:53:00 PDT
