AMBER Archive (2009)

Subject: [AMBER] drying of solvent possible ?

From: Jio M (jiomm_at_yahoo.com)
Date: Thu Aug 13 2009 - 08:49:00 CDT

Dear Amber Users ,

1) is there a way to slowly remove the water while running MD at low
temperature that is removing water only from the system keeping
solute  at last. this can be considered
as "vacuum drying of a system at low temperature (say 10'C)"

solute + Water  -------Dynamics-Run-(at low temp.)-->> solute only

2) other  question (not related to above) I want to give
environment of residue + water as a solvent to solute. Is this
correctway to provide environment of residue + water to solute. I have
run the dynamics it was successfull with no error, but I am not
confident for my procedure. I used following:

if my solute variable is "solu" and variable for residue molecule is
"res" and both saved in abc.lib

source leaprc.gaff (also loading the frcmod files of solv and solt)

loadoff abc.lib
solvateoct solu res 8.0 {this adds  res to solu }
loadoff solvents.lib
solvateoct solu TIP3PBOX 8.0
edit solu { shows water and res environment around solu}

Is this a correct method

      
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