AMBER Archive (2006)

Subject: AMBER: Post-MD minimization

From: sangeeta_at_bioinfo.ernet.in
Date: Mon Jun 19 2006 - 06:33:58 CDT

Hi Amber Community,
I have carried out an MD similations of a 13-mer peptide using GB model of
implicit solvent (with production run of 10 ns) and ff03 forcefield of
AMBER 9. The production run has completed successfully.
Now, I would like to minimize all the structures that I have saved during
the production run (10000 structures). I used the following input script
to minimize each frame:
  &cntrl
  imin = 5,
  ntx = 1,
  maxcyc = 20500, ncyc = 1000,
  ntwx = 5000, ntpr = 100, ntwr = 100,
  ntt = 1, ntb = 0, igb = 1,
  cut = 14
/

The command to run the job was specified as follows:
% mpirun -np 4 $AMBERHOME/exe/sander.MPI -O -i cga_gb_fnl_min.in -p
../../prmtop -o cga_gb_fnl_min.out -c ../cga_gb_prod10ns.rst -x
../cga_gb_prod10ns_trj.crd -r cga_gb_10ns_fmin.rst > out_cga_gb_fnl_min

I have two questions on this:
The minimization job runs fine as I can see from the .out file. However,
there are twp problems:
1. The minimization is going very very slow - on an altix machie, using 4
processors. In 48 clock hours, after submitting the job, only ~4600 frames
(out of 10000) have been minimized. There are no other jobs running on the
machine. Could there be any problem with the system so that the
minimization is going so slow? (Of course there are several "LIN-MIN
failure warnings in all coordinate set minimizations but the minimizations
appear to complete satisfactorily).

2. I would like to get the coordinates of the minimzed structures. How do
I specify this in the sander.MPI command? B'se with reference to the
previous discussions on AMBER reflector, -x is the flag for reading in the
trajectory file. I also checked the trajene files of the test set provided
with AMBER. In this set also, I could not figure out where the minimized
structrues are stored. In the minimiztion run that I am doing, even the
.rst file has not been created.

I would appreciate help in these two aspects.

Thanks a lot for your time and attention.

Sangeeta Sawant
Bioinformatics Centre
University of Pune
Pune
India

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