[AMBER] single -step transformation TI calculation

From: Victor Ma <victordsmagift.gmail.com>
Date: Fri, 9 Dec 2011 14:19:01 -0600

hi all

I was reading Dr. Steinbrecher's recent paper on comparing results from one
vs two-step transformation using the soft-core potentials. It seems as long
as right parameters were used, the single-step TI calculations is as good
as the two-step one. I'd like to try this calculation. But I'm a little
confused about how to set up the simulation.

Problem: changing REF to NEW (actually only one atom is changed in the

This is my command line: mpirun -np 2 sander.MPI -O -ng 2 -groupfile

This is my groupfile:
-O -i mdin_min_v0_l05 -o ref_min_v0_l05.out -p ref.prm -c ref.rst -r
-O -i mdin_min_v1_l05 -o new_min_v1_l05.out -p new.prm -c new.rst -r

This is my mdin_min_v0_l05 file:
  ifsc=1, crgmask=':REF',scmask=':REF',

This is my mdin_min_v1_l05 file:
  ifsc=1, crgmask=':NEW',scmask=':NEW',

This simulation went through. ( I only did the minimization as a test run).
But i'm a little confused here. I understand that for scmask, we are
disappearing REF and appearing NEW from V0 to V1. But am I doing the
crgmask the wrong way? Because I'm removing charges on REF in V0 and
removing charges on NEW in V1. Isn't that equal to changing charges from
NEW to REF? Or did I miss something here?

Thanks. Appreciate it.

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Received on Fri Dec 09 2011 - 12:30:03 PST
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