Re: [AMBER] Thermodyncamic Integration (TI)

From: emanuele falbo <>
Date: Mon, 30 Jul 2018 09:37:53 +0100

Hi David ,

Thanks for your help . I followed your suggestions , and now it works .

About the MPI , now it seems to work , probably it was due to a two wrong
topology files.

Best Regards

Il 27 lug 2018 8:05 PM, "David A Case" <> ha scritto:

> On Fri, Jul 27, 2018, emanuele falbo wrote:
> >
> > Ox + e- → Red
> >
> > by means of the TI method. Amber works well (only in serial) when the
> > solvent is not implemented explicitly. However, when I include the
> solvent
> > and ions in the systems sander doesn't work- I noticed it's because the
> > final and initial structure must have the same coordinates.
> In TI in sander, you run two simulations in parallel: they use different
> Hamiltonians but the same coordinates. So, typically, you would use the
> same coordinate file (pointed to by the "-c" flag) for both groups.
> For solvated systems, you have to make sure that the number of waters
> and ions is the same at the two end points: you cannot, for example,
> have different numbers of counterions for the two different charge
> states.
> [I don't understand why Ross and Mike decided to give these files
> different names in the tutorials. If you look, files like
> asp_model_step1.rst and asph_model_step1.rst are identical. Because
> they were using GB, leap made identical files. But the coordinates must
> be the same in both files, and this is generally done by giving the same
> file name for "-c" in both groups.]
> > 1. How do I include the solvent in the two structure keeping the
> > coordinates of the two systems equal? (Ox and Red differ only for the
> > charges).
> See above; with modern Amber, I would build the Ox (say) state and
> solvate it; then use the "change" command in parmed to create a new
> prmtop file with altered protein charges. Then you have two prmtop
> files, and one coordinate file, which is just what you need.
> >
> > 2. Why doesn't SANDER work in parallel?
> Without knowing anything other that "it didn't work", no one can
> help very much. What is the exact error message?
> ....dac
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Received on Mon Jul 30 2018 - 02:00:02 PDT
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