AMBER Archive (2008)

Subject: AMBER: WHAM: how frequently do I need data on the system coordinates?

From: David Cerutti (
Date: Thu Apr 10 2008 - 11:14:23 CDT


    I'm just starting into the wide world of WHAM, but I want to do a very
thorough study. Starting very soon, I intend to perform 10-20 simulations
for pushing biotin out of strepatvidin. My basic data collection is as

1.) 15ns total pushing run, with 0.025A perturbations every 30ps at a
1.5fs time step (1000 steps = 1.5ps)

2.) Collect data on the restraining potential with:
     &wt type='DUMPFREQ', istep1=10

3.) Write energy output data every 10 steps (0.015ps)

4.) Write coordinates every 1000 steps (1.5ps)

Is this a sufficent amount of data collection? Primarily, I'm concerned
whether my rate of coordinate output is all right, because the example in
the AMBER9 manual doesn't seem to need coordinates output at a high rate.
Since I'll have all the restart files, I could certainly go back on many
processors and resample the conformations if I needed denser sampling, but
it'd be much better to get enough readouts the first time.

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