[15-III-2013]
Hello,
Only a couple of doubts.
I am trying to run a Thermodynamic Integration calculation with Amber12 to estimate the hydration free energy of a small organic solute in explicit water solvent (TIP4PEW) under the 2-step approach (switching off the charges in the first step and then removing the vdW interactions in the second step). Actually, a similar procedure that the one in the paper by Steinbrecher, Joung and Case:
J.Comput.Chem.(2011).32(15).3253-3264
"Soft-Core Potentials in Thermodynamic Integration..."
I have already run TI calculations to transform a group of atoms into another one, but this is the first time I try to do remove a whole molecule not introducing any other one. The tutorial 9 is uselful in the first exampe but not in the second.
1) Am I right if I assume that in hydration free energy calculations:
V0 => refers the system containing solvent (common atoms) + solute (unique atoms), and
V1 => refers the system containing solvent (common atoms) only?
In that case, should it be correct to use for the V1 state just the coordinates and topology files containing ONLY the water solvent?:
V0
prmtop: solWat.top
crgmask=':solute'
scmask=':solute'
ifsc=1
V1
prmtop: wat.top
crgmask=''
scmask=''
ifsc=1
2) And also, in the in gas phase transformation ("organic molecule" in vacuo into "nothing" in vacuo), what options should I specify in V0 and V1 and what coordinate and topology files should I use for the end state?
Thank you very much!!
Kepa K.
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Received on Fri Mar 15 2013 - 10:30:04 PDT
