Dear Amber users,
I am doing a TI integration for an absolute FE calculation, and I have a
question about the procedure. I used to use the old multi-sander TI set-up,
long ago, so I am a bit rusty on this.
Imagine I want my system (in the ligand side of the alchemical cycle) to go
from (A+water) to (water). Since I am interested in absolute FE, I just
need to do decharge and vdw calculations. So, I do the following:
** decharge step:
structure of coord/parm file (in the real system there's only 1 copy of A):
1 A
2 A (same coords as previous A)
3 WAT1
4 WAT2
...
timask1 = ":1", timask2=":2", crgmask=":2", scmask1='', scmask2='''
** vdw step:
structure of coord/parm file:
1 A
2 WAT1
3 WAT2
...
timask1 = ":1", timask2="", crgmask=":1", scmask1='1', scmask2='''
Is the above correct? And is it also possible to do the vdw step in the
following way, with two copies of A?
** vdw step:
structure of coord/parm file:
1 A
2 A (same coords as previous A)
3 WAT1
4 WAT2
...
timask1 = ":1", timask2="2", crgmask=":1,2", scmask1='1', scmask2=''2'
I am thinking that, if correct, the 2nd way for vdw could be easier to
automatize.
Thanks so much!!
Ignacio
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Received on Tue Jan 17 2023 - 07:00:02 PST
