[AMBER] Soft-core alchemical transformation in TI

From: Simon Kit Sang Chu <simoncks1994.gmail.com>
Date: Mon, 23 Jul 2018 23:11:35 +0800

Hi everyone,

I am planning to transform a methanol into an ethanol. I did a simulation
of pure methanol solvated in water. I want to keep all the coordinates and
velocities, including common hydrogens, in the restart in amber format. I
have two concerns right now.

First, to transform from methanol to ethanol, I have to cut a hydrogen out
from methanol and append a CH3- from the broken end. I briefly look into
AMBER manual and dummy atoms are necessary for pmemd preparation. Atoms
transformed must also have the same masses so I cannot transform the
hydrogen truncated into the new carbon. In that case, how should the
coordinate files be written? Can I skip creating a pdb with a crd and
include the hydrogens?

Second, I am new to AMBER and I am not sure if it is using dual topology.
If so, the CH3- will still be bonded with methanol while having no LJ and
electrostatics. However, will the thermal motion created by the thermostat
alter the motion of methanol even at lambda = 0? If I am transforming a
methanol to a hexanol, the methanol motion would largely be random due to
the higher momentum of the "invisible" (CH2)4-CH3 tail.

I appreciate any advice. Sorry for the long mail!

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Received on Mon Jul 23 2018 - 08:30:02 PDT
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