[15-IV-2013]
Hi everybody,
Well, actually the questions in this email are intended for Dr. Thomas Steinbrecher but I thought that the answers might be also useful for other amber users so I posted it here in the amber reflector instead of emailing him directly.
I am running a TI calculation to determine the hydration free energy of my solute "ANQ" (glutamine side chain analogue) in water (TIP4PEW) following the steps in:
"Soft-Core potentials in Thermodynamic Integration: comparing One- and Two-step Transformations"
J. Comput. Chem. 32: 3253-3263 (2011)
I would like to check that I am actually using amber12 TI tools correctly (by reproducing the energy of the same calculation in that paper) to be sure that I am correctly using TI to apply it later to different systems I will be studying.
The V0 state includes the solute in water and the V1 state is only the water box. I defined the system like this:
V0 => [anqWAT.top/rst] solvent "WAT" (common atoms) + solute "ANQ" (unique atoms)
V1 => [anqBOX.top/rst] solvent "WAT" (common atoms) only
I wanted to run a 1-step transformation, removing the charges and the Van der Waals interactions all at once using soft-core potentials in both cases (coulomb + vdW), to make disappear the solute from the solvent box (I would like to avoid the gas-phase step necessary for the 2-step transformations).
I have defined my input files like this:
=> Common part of the Input file for V0 and V1:
Step 3. NPT TI production-sampling in Water.
&cntrl
imin=0, nmropt=0,
ntx=1, irest=0, ntrx=1,
ntxo=1, ntpr=500, ntwr=500,
iwrap=0,
ntwx=500, ntwv=0, ntwe=500,
ntf=1, ntc=2, ntb=2,
ntp=1,
igb=0, nsnb=25, cut=9.0,
nstlim=1000000, nscm=500, nrespa=1,
t=0.0, dt=0.002,
vrand=0, vlimit=20.0,
ig=${RANDOM}, ntt=3, gamma_ln=2.0,
temp0=298.0, tempi=298.0, tautp=0.5,
pres0=1.0, taup=2.0,
tol=0.00001,
icfe=1, clambda=0.${X},
scalpha=0.4, scbeta=7.84,
=> V0.in
ifsc=1,
scmask=':ANQ',
crgmask=':ANQ',
noshakemask='',
/
=> V1.in
ifsc=1,
scmask='',
crgmask='',
noshakemask='',
/
1) Doing this I find that sander removes the charges from the solute from the very beginning (V0) and therefore the whole calculation is run as if the solute did not have any charges during all the lambda-values from 0.01 to 0.99. Am I right? If yes,
a) Should I just leave the "crgmask" in blank in V0 and V1 and sander will deal with the charge automatically?
b) in the paper it is said that SHAKE algorithm is used to constraint hydrogens. Is SHAKE also used in the solute? I am asking this because I thought that shaking the part of the system that experiments the alchemical transformation was not a good idea since the partition function is modified (by constraining the stretchings), and therefore the free energy might be also affected for it.
2) Are the other options in the input files OK for the calculation I am trying to run?
Kind regards.
Kepa K.
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Received on Mon Apr 15 2013 - 05:30:04 PDT
