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,
> 1/61 Henry Wellcome Building , University of Leicester,
> Lancaster Road,
> Leicester,
> LE1 7RH
>
> T: 0116 229 7237
> E: k.sidhu.le.ac.uk<mailto:k.sidhu.le.ac.uk>
>
> [cid:151BE3D7-8FA6-433C-911F-5620E921A339.le.ac.uk]
>
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Received on Fri Mar 18 2016 - 13:00:03 PDT
