AMBER Archive (2008)

Subject: Re: AMBER: ptraj & imaging of velocities

From: Lars Skjærven (lars.skjarven_at_biomed.uib.no)
Date: Tue Sep 02 2008 - 08:15:49 CDT

Hi,
Use your last working restart file to do one step of MD with iwrap=1.
You can then use this new restart to continue your simulation. Thats
what you want I guess...(?)
Lars

On Tue, Sep 2, 2008 at 3:06 PM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
> Dear Amber users,
>
> We got **** characters in a restrt file (MD simulation carried out using
> iwrap=0; Amber 8); consequently our MD simulation crashed. This problem has
> been already reported in the Amber mailing list. As we save restrt files
> each nsec, we used a previous restrt file (without **** characters) to
> re-image the corresponding Cartesian coordinates using ptraj (& to re-run
> the MD simulation using ntx = 5, irest = 1). However, in this case the
> velocities are set to zero by ptraj...
>
> Is it correct to re-image the velocities (derivative) as we re-image the
> Cartesian coordinates using ptraj ? (in this case, we have to change the
> order Cartesian coordinates - velocities in the restrt file; see below)
>
> Thank you, regards, Francois
>
>
> Step 1:
> ptraj
> "restrt-a1" ----> "restrt-b"
> Cart. coord re-imaged Cart. coord
> velocities set to zero: do not use them
>
> Step 2:
> ptraj
> "restrt-a2" ----> "restrt-c"
> velocities (*) re-imaged velocities
> Cart. coord set to zero: do not use them
>
> (*) manually change the order "Cart. coord" <--> "velocity" in the restrt
> file
>
>
> Step 3:
> "restrt-b" manually
> ---> "restrt-d"
> "restrt-c" re-imaged "Cart. coord + velocities"
>
>
>
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