On Sun, Dec 16, 2012 at 7:53 AM, <tommaso.casalini.mail.polimi.it> wrote:
> Dear Amber users and developers,
> I have a problem when Amber tries to read the .rst file in order to
> continue a simulation from another one.
> I am simulating a very big system (the average edge value of the cubic
> simulation box is equal to 190) and I have some very fast particles
> which diffused far away from the simulation box. However, I cannot use
> the command "iwrap=1" since my simulations are aimed at computing a
> self-diffusion coefficient.
> In the .rst file, some values are substituted with a series of '*' and
> thus amber cannot read properly the restart file as input. I tried to
> use the command "ioutfm=1" but it seems to affect only .mdcrd files
> and not the .rst files, as user manual says.
> I would like to ask you if you have some suggestions, because now I
> cannot continue the simulation, and you can understand that it is a
> big problem.
> I am using AMBER11 version, but I have access also to AMBER12, if it
> is necessary.
> I thank you in advance for your help and collaboration.
>
There is an "unwrap" command in cpptraj and ptraj if you set iwrap=1. Of
course, IMO the best solution is to use binary (NetCDF) restart files.
These became available in Amber 12 (so you would have to switch to Amber
12). The option is not in the Users' manual, but it has been posted as an
errata on
http://ambermd.org/doc12/
With binary restart files, there are no silly limitations on the size of
the coordinates :).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Dec 16 2012 - 07:00:03 PST
