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

From: Hamed S. Hayatshahi <>
Date: Tue, 10 Sep 2013 12:35:54 -0700 (PDT)


Thanks. It was a key help and made a big difference. 
Now I did the same thing with scalpha = 0.2, scbeta = 2.5 (as optimums from the paper) and got Total DV/DL: 657.586725+-26.099875 after integration which is above the resulted value in the paper. The differences in my practice were:

1- I did a 9 window (0.1-0.9) lambda.
2- I did two steps of heating/equilibration (constant volume then constant pressure), based on Insuk and Cheatham 2008 paper and a production run of 200ps. 
3- I had a truncated octahedral water box with 809 water residues. 

By the way, the dv/dl values are as follows which I am not sure if their trend seems normal or not.

lambda    dv/dlrms
0.1     645.6251        18.5543
0.2     1720.7175       81.3843
0.3     1211.1193       27.0231
0.4     892.4151        20.4867
0.5     687.2261        18.3589
0.6     543.1469        17.7574
0.7     433.1750        17.2522
0.8     338.6250        18.4672
0.9     243.9317        21.6250

Which factor do you think has caused the difference in resulting energy? 

Thanks again; 
Hamed S. Hayatshahi
PhD candidate in Medicinal Chemistry
University of Utah
+1 801-867-4501


 From: "" <>
To: Hamed S. Hayatshahi <>; AMBER Mailing List <>
Sent: Sunday, September 8, 2013 10:56 AM
Subject: Re: [AMBER] TI input files in A9 tutorial and Amber12 manual


> For example, in the one-step Mg+2 system, you had an ion-containing water
> box as V0 and the same water box without ion as V1; and both crgmask and
> scmask masks were ':Mg+' for V0 and ' ' for V1. This, both vdW and charge
> interactions for the ion are expected to change from Mg+ parameters to
> nothing. Am I understanding it correctly? And so the integration over
> DV/DL values over the 99 windows on this one step added up to ~414
> (according to table 3), right? 

Almost. crgmask was set to '' in V0 as well, otherwise you strip the
magnesium charge before any calculations start and effectively let an
uncharged magnesium-sized particle disappear.

V0: scmask='MG', crgmask=''
V1: scmask='', crgmask=''

you let a charged magnesium disappear completely, treating both its charge
and vdW interaction via soft-core potentials.

Kind Regards,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Tue Sep 10 2013 - 13:00:03 PDT
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