AMBER Archive (2002)

Subject: dump coordinate into mdcrd

From: A. Hungie (hungie01_at_hotmail.com)
Date: Fri Aug 30 2002 - 03:03:17 CDT

Dear All,

I would like to run MD simulation from 0-1010 ps and dump coordinates into
mdcrd file after the 1000th ps (i.e. 1000-1010 ps, total 10 ps). As I know,
in sander_classic, we can control by setting ntwxm=1000, but ntwxm is no
longer present in sander. Could you please tell me how to control dumping
snapshot in sander? I am using AMBER 6. The point is that I would like to
dump coordinate every 2 fs which needs more disk space. Therefore I can't
start to dump coordinates since beginning of the simulation.

I have tried to run 2 simulations.
First (namely run_A), run 0-1010 ps (coordinates were dumped every 1 ps).
Second (namely run_B), run 0-1000 ps (no coordinate was dumped), then used
"restrt" file of the 1000th ps to run for 1000.002-1010.000 ps (dumping
every 2 fs, total 5000 snapshots).
However, I have a problem. When I compared results (energy and coordinates)
for 1000-1010 ps given by run_A and run_B, they were different corresponding
to the same time (e.g. at 1005 ps (run_A) and 1005.000 ps (run_B) they were
not identical results).

As I understand, I can't get the same result when I do a simulation in one
step comparing with 2 steps. For instance, one step 0-200 ps versus two
steps 0-100 ps and 101-200 ps, The last 100 ps will be different.

Therefore the best way is that I have to do simulation in one step, and dump
coordinates only in a period I want, but I don't know how to do this.

Thank you very much in advance.

Regards,
Hungie

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