Re: [AMBER] restart file error

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Fri, 18 Mar 2016 12:47:01 -0700

Have you looked at the values in mdout? There would normally be signs of
the simulation blowing up there. What equilibration protocol did you
use? (E.g. paste in your mdin files.)

Bill

On 3/18/16 3:59 AM, Sidhu, Khushwant (Dr.) wrote:
> Hi,
>
> when I try to restart a simulation from a restart file (I’ve rerun & written multiple ones), I get the following in most of them
>
> cat tstar-25N_mdrun3.rst_39000000|grep "*"
> 109.8620092-180.0417570 558.6467279************ -94.5936925 39.7954818
> ************ -94.6608645 40.2439769************ -94.6238634 40.4988053
> ************ -94.6040732 39.9183133-103.9120614 501.3300167 -51.3830672
>
> My input file is as follows:
>
>
> production run protocol
> &cntrl
> imin=0, irest=1, ntx=5, ig=-1, ioutfm=1,
> nstlim=40000000, dt=0.002,
> ntc=2, ntf=2,
> ntb=2, cut=8.0,
> ntp=1, taup=2.0,
> ntpr =10000, ntwx=50000, ntwr=-50000, ntwv = -1
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> /
>
> cheers
>
> Sid
>
> ------------------------------------------------------------------------------------
>
> Dr Khushwant Sidhu
> Senior Experimental Officer / I. T. Professional
>
> Department of Molecular and Cell Biology,
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> Lancaster Road,
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>
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> E: k.sidhu.le.ac.uk<mailto:k.sidhu.le.ac.uk>
>
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>
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Received on Fri Mar 18 2016 - 13:00:03 PDT
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