Good day
Thank you very much
Regards
Tebello
On 15 November 2016 at 21:24, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Nov 15, 2016 at 11:32 AM, Tsibela German Tebello Mofokeng <
> 1754789.students.wits.ac.za> wrote:
>
> > Good day
> >
> > I would like to run a constant pH MD calculation but i do not have the
> > jobfile (.pds) submission script and the input (.in) script.
> >
> > I have managed to create the following files:
> > full minimization (Full_mini.rst, Full_min.out); heating stage
> > (Heat_stage.out, Heating stage.rst); equilibration (equil.out,
> equil.rst).
> >
> > Now I would like to perform constant pH MD calculations, could you please
> > help me with a submision (.pbs) and input (.in) scripts for constant pH
> MD
> > calculations.
> >
>
> This is not really something we can help with. Each computer cluster will
> have a slightly different set of options and syntax for specifying
> resources than any other cluster, with different policies. Typically, a
> cluster will have documentation with sample job files to serve as examples
> you can build off of. We are not the right resource for asking questions
> about a queuing/scheduling system for whatever cluster you happen to be
> using.
>
> As far as input files are concerned, those are also dependent on exactly
> what you are trying to do. And you have not given nearly enough
> information to guess what your input file should look like in its
> entirety. Do you want implicit solvent? Explicit? etc.
>
> I would highly recommend working through some of the tutorials (the
> constant pH one in implicit solvent
> http://ambermd.org/tutorials/advanced/tutorial18/ and explicit solvent
> http://jswails.wikidot.com/explicit-solvent-constant-ph-md) so you develop
> an improved understanding of what options are available. This will help
> you build your own input files more effectively.
>
> HTH,
> Jason
>
> -
> -
> Jason M. Swails
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Received on Wed Nov 16 2016 - 01:30:02 PST
