Hi Anthony,
Go back to the previous good restart file and re-run it but in the input
file select iwrap=1. This will wrap everything back into the central box and
deal with the issue of waters having diffused too far from the central box.
1 step is good enough. Then you can set iwrap=0 again and continue your run.
Alternatively you can leave iwrap=1 for your entire run and avoid this
simulation but note it can cause issues with calculating RMSD, diffusion
constants etc, especially if your solute diffuses out of the central box.
Good luck.
Ross
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Anthony Cruz
> Sent: Wednesday, September 26, 2007 07:56
> To: amber.scripps.edu
> Subject: AMBER: Simulation continuation problem. Cant read
> restart file!!!!!!
>
> Hi User:
> I have been wotking with a simulation of a heme protein in
> water. I decide to
> run the simulation in multiple steeps of 500 ps. Right now I
> have 116 part
> of 500ps (aprox. 60 ns). The problem is that when I re-start
> the simulation
> to do other 5ns of simulation the simulation stop because one
> of the parts
> cant read the box or the restart file from the previous part.
> When I check
> the file I found the some of the coordinate were written as
> *. I restart all
> the parts again and have the same problem again. How I can
> resolve the
> problem of the coordinates in the restart file???
>
> Best regards,
> Anthony
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Received on Sun Sep 30 2007 - 06:07:12 PDT
