From: Hannes Loeffler <>
Date: Wed, 28 Jan 2015 10:34:47 +0000

On Wed, 28 Jan 2015 11:10:45 +0100
Federica Chiappori <> wrote:

> Dear all, thank you for your answers and suggestions.
> Finally, I will perform TI as explained in the amber14 reference
> manual. I'm employing pmemd to perform these simulations because I'm
> using a GPU server.
> In the reference manual is described how to obtain a single topology
> file for wt and mutant proteins, but there is not described how does
> the group file looks like (pag. 351). In particular: mdin and prmtop
> are the same files for both lines and only the outputs are different,
> are both line necessary? Or with the new commands (timask and scmask)
> I will obtain all the informations in a single file?

You have to be careful understanding how this is implemented at the

Both pmemd and sander can do TI (compatible code) but the user
has to handle prmtops(s) in a different way. While pmemd14 needs only
one topology file (be careful calling this 'sinlge topology' because
this term refers to a particular method implementation of this kind of
simulations), sander needs two prmtops and, as you will be using the
multi sander facility, also a group file. Pmemd does not use group
files. Also, pmemd's TI code does currently not run on GPUs.

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Received on Wed Jan 28 2015 - 03:00:02 PST
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