AMBER Archive (2006)

Subject: RE: Re: AMBER: A question about Dynamics.

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Sep 21 2006 - 10:58:08 CDT

Dear Shu,

> Thank you for your reply. But I checked the .in files again.
> There is no problem. And I found that even the
> temperatureVs.time plot had a drop. Following is the two .in
> files. Thank you.
>
> SHU
>
> md0.in
> &cntrl
> IREST=0, NTX=1,
> igb=1, NTPR=200, NTWX=200,
> ntt=3, gamma_ln=1.0,
> NTR=1, TEMPI=0.0,
> NTB=0,
> TEMP0=300.0,
> NTP=0,
...

This is not enough information for us to help you. What command line options
did you use, what size was the energy drop? If you compare the final output
from the first trajectory and the first output from the new trajectory where
are the differences?

Have you changed the structure you are restraining to? E.g. did simulation 1
restrain to the initial inpcrd file and then simulation 2 restrain to the
restart file from simulation 1? In this case the discontinuity in the
potential energy will be due to the restraint energy changing.

As Dave suggests take a 'careful' look at the output from your two
simulations. Set up the new run to do only 1 step so that you get the
energies for the first structure in this simulation. Then compare every
energy term with the final results from the previous simulation. This will
tell you where to start looking to explain what is going on.

All the best
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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