Re: [AMBER] ptraj, unit cell wrapping and velocities

From: Ben Roberts <roberts.qtp.ufl.edu>
Date: Wed, 29 Sep 2010 13:59:42 -0400

Hi Dave,

> You should never need to "wrap" velocities, as far as I know. But it's easy
> enough to check: run short simulations with and without imaging of
> coordinates, and see what happens.

True enough. And, indeed, I find that the velocities are pretty similar.

For interest's sake, here are the numbers:

Step # Max diff RMS diff
------ -------- --------
 1 0.0002274 0.0000364
 2 0.0004390 0.0000698
 3 0.0006116 0.0000981
 4 0.0007483 0.0001199
 5 0.0008979 0.0001349
 6 0.0011089 0.0001438
 7 0.0012832 0.0001480
 8 0.0014209 0.0001497
 9 0.0015147 0.0001515
10 0.0015537 0.0001554

Given these small differences, I've decided it's safe to copy and paste the velocities from the unwrapped file into its wrapped counterpart.

Cheers,
Ben
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Received on Wed Sep 29 2010 - 11:30:04 PDT
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