AMBER Archive (2003)

Subject: Re: AMBER: umbrella sampling with AMBER

From: David A. Case (case_at_scripps.edu)
Date: Mon Dec 22 2003 - 19:48:30 CST

On Mon, Dec 22, 2003, Mey Khalili wrote:
>
> I am trying to do umbrella sampling for flipping a proline from cis to
> trans in ribonucleaseA. I have already a 600ps explicit solvent
> equilibrium dynamics of the wildtype (P93 CIS). I use ptraj and use the
> trajout filename restart command to take the 600 ps snapshot and make it a
> restart file. I think the first problem arises here. Because when I look
> at the restart file, all the waters at the end have coordinates zero (I
> have not specified for the waters to be excluded).

Are you sure it is the waters that have zero coordinates, and that you are
not looking at the velocities? When ptraj tries to make a restart file,
it doesn't have any velocity info, and (I think?) sets them to zero. The
first 3N numbers in the restart file are the coordinates, the second 3N are
the velocities.

If you have a 600 ps trajectory, why not use its restart file, rather than
trying to make one from ptraj?

>
> and then it hangs there.When I run it on Lemieux supercomputer in
> Pittsburgh, it goes all the way to the same place and then it complains that
> NMROPT is not zero and it can't reorder the waters.

You need to recompile sander, leaving out the -DROWAT -DRLE options; this is
the only thing that will allow you to run with nmropt=1. There will be a
slight but not great loss of parallel speedup, but this should not be a real
worry. [I think pmemd would also work, but you would want at least a test
run in sander in order to be sure; if the results are the same, pick which
ever one runs faster.]

...good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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