Hi Cao,
This can happen quite often and is normally due to waters diffusing over a
long trajectory. It happens a lot when running Langevin dynamics. The
solution is to go back to the last good restart file that you have. Set
iwrap=1 in the &cntrl name list and run from there. This will
automatically image atoms back into the central box and will thus avoid
the *'s in the restart file.
All the best
Ross
On 10/8/12 2:08 PM, "Cao Yang" <muxiachuixue.163.com> wrote:
>Hi all,
>
>
>I came across a problem with my MD recently. The system is a membrane
>protein containing about 70,000 atoms and was simulated with AMBER11. The
>following is the input file of production phase.
>
>
>production hSGLT2_dpp
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=5812000,dt=0.002,
> ntc=2,ntf=2,
> cut=10.0, ntb=2, ntp=2, taup=2.0,
> ntpr=1000, ntwx=1000,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> /
>
>
>When the job went to 38ns, some asterisks appear in the restart file.
>That leads to the impossibility of restarting the job. Now the only thing
>I can do is to avoid breaking the calculation. I copied some of the data
>in the rst file.
>
>
> 59.7272199************ 137.8027357 -59.5537208************ 138.0484368
> 60.4061406************ 138.4130880-156.4547856 88.0830801 142.243969
>
>My question is:
>Why did this problem arise and how should I fix it?
>
>
>Many thanks!
>
>
>╔════════════════════════╗
> Cao Yang, Master,
> Department of Medical Chemistry,
> College of Pharmaceutical Sciences,
> Zhejiang University,
> Hangzhou, China
> Email: muxiachuixue.163.com
>╚════════════════════════╝
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Received on Mon Oct 08 2012 - 06:00:08 PDT
