Hi
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: "steinbrt.rci.rutgers.edu" <steinbrt.rci.rutgers.edu>
To: Hamed S. Hayatshahi <susan_wasson.outlook.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Sunday, September 8, 2013 10:56 AM
Subject: Re: [AMBER] TI input files in A9 tutorial and Amber12 manual
Hi,
> 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.
With
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,
Thomas
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
