Re: [AMBER] amber - TUTORIAL A9

From: <>
Date: Sun, 4 Dec 2011 14:54:16 -0500 (EST)


> For each transformation and in each substep 1->4, 2->5 and 3->6, I should
> do minimization,
> equilibration<>
> and production
> <>for each
> lambda.

yes, that is correct. minimization, equilibration and production are
consecutive of course.

> You pointed only to bnz_prod_v0_lx.out ( x= 1,2,3,4,5,6,7,8,9) and not
> to
> bnz_prod_v1_lx.out. why?
> Are bnz_prod_v0_l1.out file and bnz_prod_v1_l1.out file identical?

for a charge removal they would be identical. If ifsc is set to one, the
output will differ (since different softcore region are used) but the
output files still give the same dvdl and that is the main information you

> Do not need to use bnz_min_v0_l1.out or bnz_equi_v0_l1.out files?

not to get dvdl, you would need them in a real study to check that your
simulation went ok though. the dvdl values in there would probably be
unused though.

> How do you obtain these data from *.out files?
> For example, DVDL = -5.424

well, reading the output file is one option ;-) There is a result summary
at the end where you can get the average dvdl and its rmsd value. Of
course, for many files you would write a script to collect the information
for you.

Kind Regards,


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

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Received on Sun Dec 04 2011 - 12:00:04 PST
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