Re: [AMBER] TI input files in A9 tutorial and Amber12 manual

From: Hamed S. Hayatshahi <>
Date: Wed, 4 Sep 2013 15:02:32 -0700 (PDT)

Thanks for all the hints. I could set up the TI with ifsc=1 for a one-step change in which both charge and vdw change simultaneously, but I want to make sure I am doing it in the right way! I think part of the confusion arises from not well-described (or understood) differences between ways we can do TI, particularly how to use soft-core potentials. So I am still trying to make it clear for myself and request you to correct me:
Based on putting together the manual, A9 tutorial and some highlighted references, it seems that three ways of doing TI are described: 

1) No soft-core potentials with need to dummy atom; and changing the charge and vdw in different steps as discussed in part 4.1.1 of the amber12 manual.
2) Soft-core potential used only in changing the vdw; and changing the charge and vdw in different steps in which no dummy atom is needed; as discussed in tutorial A9.
3) Soft-core potential used in changing the charge and vdw simultaneously in a single step with no dummy atom needed; as discussed in part 4.1.2 of the amber12 manual . 

This way, A9 tutorial seems to me like a transient intermediate method between the methods introduced in part 4.1.1 and 4.1.2 of the manual. This is because it changes the charge and vdw in different steps while using sof-core potential in just one step out of three. Furthermore, it seems that amber12 doesn't like parts of A9 where ifsc=0 while the coordinate and mdin files are set to be different for two ends of a step (V0 and V1), as expected from the manual 4.1.1. (as Dr. Cheatham says, tutorial might be out of date for amber12)

Also, better for both the manual and tutorial to be more clear about the difference between crgmask and scmask. Does scmask apply only when ifsc=1? Should them be the same when using the soft-core potential to simultaneously change the charge and vdw? 

Sorry for the long and maybe confusing discussion. Hopefully this makes the things more clear for others as well.  

Hamed S. Hayatshahi
Graduate Student of Medicinal Chemistry
University of Utah
+1 (801) 807 4121


 From: David A Case <>
To: Hamed S. Hayatshahi <>; AMBER Mailing List <>
Sent: Friday, August 30, 2013 1:45 PM
Subject: Re: [AMBER] TI input files in A9 tutorial and Amber12 manual

On Fri, Aug 30, 2013, Hamed S. Hayatshahi wrote:
> I am trying to do a simple TI (disappearing of a cation in a water
> box) with Amber12 sander using softcore potential. I have a couple of
> confusions: 
> 1- The A9 tutorial sets up different crgmask values for V0 and V1
> processes, thus making different mdin files and also different starting
> coordinates, leading to a group file like this (from the liked shell
> script):
> -O -i mdin_min_v0_l${X} -o ${pre0}_min_v0_l${X}.out -p ${pre0}.prm -c ${pre0}.rst -r ${pre0}_min_v0_l${X}.rst
> -O -i mdin_min_v1_l${X} -o ${pre1}_min_v1_l${X}.out -p ${pre1}.prm -c ${pre1}.rst -r ${pre1}_min_v1_l${X}.rst
> But under the related topic, page 114 of the manual clearly says: "The
> input (mdin) and starting coordinate files must be the same for the
> two groups".

I agree that the manual is a little confusing, but a careful reading
of section 4.1 will help.  The second paragraph there starts by saying
that there are two ways of proceeding: the first requires the prmtop
files to have the same number of atoms, etc.  Later, this paragraph says
that "Alternatively," you can use the softcore algorithm **described
below**.  The text that immediately follows (which you quote) then refers
to the first option.  All further information about the softcore option is
"below" (in section 4.1.2).

The tutorial is using the softcore model described in Section 4.1.2, and you
should refer the the description there, which specifically talks about how
the two mdin files can differ (see the description of "scmask").

[Thanks for your report: we will make the manual clearer about the
distinction between the two alternatives in the next release.  This will
be doubly important since there will then be yet more ways to do TI.]

> Also when I use different mdin and/or starting coordinate
> files, sander.MPI crashes with the following last lines in the output: 
> | MPI Timing options:
> |      profile_mpi =        0

We would need more information to help with this error.  I don't think it
has anything directly to do with the fact that the mdin or coord files are
the same or different.


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Received on Wed Sep 04 2013 - 15:30:02 PDT
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