AMBER Archive (2006)

Subject: Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Aug 23 2006 - 07:18:03 CDT

what value of nscm did you use?

priya priya wrote:

> Sir
> I have looked into the rst file there are many *'s.
> Firstly i took nstlim=2500000, dt=0.002.
> as per ur suggestions i reduced the nstlim to 500000 with dt = 0.001,
> that also didnt worked out.i am still getting the *'s in the rst file.
> Now i have again run the simulations with nstlim=10000, dt=0.002.i am
> running the system in implicit solvent.
>
> Please do suggest me.
>
> With Regards
>
> Priya Anand
>
> */Ross Walker <ross_at_rosswalker.co.uk>/* wrote:
>
> Dear Priya,
>
> Have you looked at the restart file to see if you can see what is
> wrong with it. Are there any *'s in the output file suggesting
> that your system drifted away from the original origin by too far?
> Have you visualized the trajectory? Does anything look wrong? Did
> your system blow up or did it remain stable?
>
> Check if you set nscm to a reasonable value. If you are running
> this system in implicit solvent you probably need to set nscm=1000
> or so to remove center of mass motion. Without doing this your
> system can drift a long way from the origin such that the
> coordinate values exceed the available space in the output and
> restart files.
>
> Alternatively your restart file may have simply got corrupted due
> to hardware issues with your computer system. Without more details
> about the specific problem we can't help much more I am afraid.
>
> All the best
> Ross
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP
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>
> ------------------------------------------------------------------------
> *From:* owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] *On Behalf Of *priya priya
> *Sent:* Monday, August 21, 2006 00:46
> *To:* amber_at_scripps.edu
> *Subject:* AMBER: problem relating all atom structure
> prediction and folding simulations on AMBER8
>
> Dear
>
> I am doing the first stage of the simulation on 42 residue
> peptide at 325 K. Running 50 ns of simulation at 325 K in 10
> stages of 5 ns each.
>
> Input file reads as follows:
>
>Stage 2 equilibration 1 0-5ns &cntrl imin=0, irest=1, ntx=5, nstlim=2500000, dt=0.002, ntc=2, ntf=2, ntt=1, tautp=0.5, tempi=325.0, temp0=325.0, ntpr=500, ntwx=500, ntb=0, igb=1, cut=999.,rgbmax=999. /
>
>The commannd used for running simulation is
>
>$AMBERHOME/exe/sander -O -i equil.in -p TC5b.prmtop -c heat7.rst -r equil1.rst -o equil1.out -x equil1.mdcrd
>
>first step run well for 5 days but the rst file is not complete. when i run the next step of 5ns it gives an error as
>
>forrtl: severe (64): input conversion error, unit 9, file /usr/local/amber8/exe/equil1.rst
>
>so now i am unable to proceed further will be somebody guide
> me.
>
>With Regards
>
>Priya Anand
>
>Department of Biophysics
>
>Panjab University
>
>Chandigarh.
>
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