AMBER Archive (2006)

Subject: Re: AMBER: Post-MD minimization

From: Carlos Simmerling (
Date: Mon Jun 19 2006 - 09:27:37 CDT

If the structures were generated using the same conditions
as you are using for minimization (same gb, etc) then I see
no reason at all for each structure to have linmin errors.
What do the initial energies in the minimization look like?
carlos wrote:

>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 -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
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