Re: [AMBER] Help Constant pH MD calculations

From: Jason Swails <>
Date: Tue, 15 Nov 2016 14:24:25 -0500

On Tue, Nov 15, 2016 at 11:32 AM, Tsibela German Tebello Mofokeng <> 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

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 and explicit solvent so you develop
an improved understanding of what options are available. This will help
you build your own input files more effectively.


Jason M. Swails
AMBER mailing list
Received on Tue Nov 15 2016 - 11:30:02 PST
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