Thanks Dan!
Could someone suggest me some unix utility useful for the conversion of the
amber's trajectory format to the charm-like .dcd ?
James
2014-05-20 19:57 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> On Tue, May 20, 2014 at 9:05 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
> > Firstly I'd like to know about possibility to generate *.rest file
> > (consisted of coordinates +felicitates +box vectors in specified time
> step)
> > from selected step of the output trajectory or md.out file. For instance
> > one of my recent simulations have been crashed and broken check point
> file
> > have been created so I'd like to restore it manually.
>
> You can restore coordinates from a trajectory file, e.g.
>
> trajin input.nc 30 30 # selects frame 30 only
> trajout restart.rst7
>
> but unless you were also writing velocities (i.e. ntwv != 0) you
> cannot create a true restart file. If you have a separate velocity
> trajectory you can use those velocities with the 'mdvel' keyword, e.g.
>
> trajin input.nc 30 30 mdvel vel.nc
>
> or if you wrote a combined coordinate/velocity trajectory (NetCDF
> only) the velocities will be read in automatically.
>
> You can generate random starting velocities for a new MD run according
> to a temperature distribution by running with irest=0, ntx=1, and
> ig=-1.
>
> Hope this helps,
>
> -Dan
>
> >
> > James
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 21 2014 - 08:30:02 PDT
