Holly,
I don't have time to dig in details here, but my hunch is that your
problem is NOT related to the particular mutation you're doing, but
rather something more fundamental. The particular places I'd look are,
in order:
(1) See about adding more lambda points. In my experience even with
five point TI for the charging energies one gets significant (i.e.
~0.2-0.5 kcal/mol) integration error even when leaving the net charged
fixed (i.e. for the charging free energy of SPC water in SPC water),
say roughly a 5-10% error. I could easily imagine that using three
point integration for something where the magnitude is more than 20
kcal/mol could give you at least 3 kcal/mol of integration error. 9
points is also few for the LJ part -- but adding more points won't
make as big a difference in the total answer since the net LJ
component is usually fairly small and should be similar for these two
molecules.
(2) Maybe send along your values for the LJ component. One would
expect this to be small (~0.5 kcal/mol?) so if it's not, that would be
a sign of some sort of problem there.
Thanks,
David
On 10/22/07, Holly Freedman <freedman.phys.ualberta.ca> wrote:
> Hi Thomas,
>
> Thank you for taking the time to look at my input and for your suggestions. I will try changing the
> ntf, but this shouldn't effect interaction with water that much should it? I have pasted below the
> input files for the soft-core step. I looked at the trajectories and they seem OK. I don't have any
> experimental data to compare to, unfortunately. The free energy curves look pretty smooth, the
> charging ones are linear and the charging energies can pretty much be determined just from the
> lamdba = 0.5 simulations.
>
> I am thinking that I would be better off letting the perturbation be from OCH3 to OH, charges on and
> off OH and OCH3, rather than on and off H and CH3 and changing CH3 to H. This should work
> better because in this case the molecule won't gain too large a charge when the partial atomic
> charges are turned off since the OCH3 and OH groups should be closer to neutral than CH3 and H
> (the overall charges of the molecules are all neutral). In this case I shouldn't have to use a noshake
> mask at all, should I ? What do you think about this plan?
>
> Thanks,
> Holly
> --
> Department of Physics, University of Alberta
> Edmonton CANADA
>
> Files for perturbation in water:
>
> &cntrl
> imin = 0,
> ntx = 5, irest = 1, ntr = 0, iwrap=1,
> ntpr = 100, ntwr = 100, ntwx = 5000, ntwe = 5000,
> ntf = 2, ntb = 2, cut = 10,
> nstlim = 500000, dt = .002, ntc = 2,
> tempi = 298.0, temp0 = 298.0, ntt = 3, gamma_ln = 2,
> tautp = 1.0, ntp = 1,
> icfe = 1, clambda = 0.01592, klambda = 1,
> ifsc = 1, crgmask = ':1.H10',
> scmask = ':1.H10', noshakemask = ':1.H10',
> &end
>
> &cntrl
> imin = 0,
> ntx = 5, irest = 1, ntr = 0, iwrap=1,
> ntpr = 100, ntwr = 100, ntwx = 5000, ntwe = 5000,
> ntf = 2, ntb = 2, cut = 10,
> nstlim = 500000, dt = .002, ntc = 2,
> tempi = 298.0, temp0 = 298.0, ntt = 3, gamma_ln = 2,
> tautp = 1.0, ntp = 1,
> icfe = 1, clambda = 0.01592, klambda = 1,
> ifsc = 1, crgmask = ':1.C3,H10,H11,H12',
> scmask = ':1.C3,H10,H11,H12', noshakemask = '',
> &end
>
> Files for perturbation in the vacuum:
>
> &cntrl
> imin = 0,
> ntx = 5, irest = 1, ntr = 0, iwrap=0,
> ntpr = 100, ntwr = 100, ntwx = 5000, ntwe = 5000,
> ntf = 2, ntb = 0, cut = 10,
> nstlim = 100000, dt = .002, ntc = 2,
> tempi = 298.0, temp0 = 298.0, ntt = 3, gamma_ln = 2,
> tautp = 1.0, ntp = 0,
> icfe = 1, clambda = 0.01592, klambda = 1,
> ifsc = 1, crgmask = ':1.H10',
> scmask = ':1.H10', noshakemask = ':1.H10',
> &end
>
> &cntrl
> imin = 0,
> ntx = 5, irest = 1, ntr = 0, iwrap=0,
> ntpr = 100, ntwr = 100, ntwx = 5000, ntwe = 5000,
> ntf = 2, ntb = 0, cut = 10,
> nstlim = 100000, dt = .002, ntc = 2,
> tempi = 298.0, temp0 = 298.0, ntt = 3, gamma_ln = 2,
> tautp = 1.0, ntp = 0,
> icfe = 1, clambda = 0.01592, klambda = 1,
> ifsc = 1, crgmask = ':1.C3,H10,H11,H12',
> scmask = ':1.C3,H10,H11,H12', noshakemask = '',
> &end
>
>
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Received on Wed Oct 24 2007 - 06:07:47 PDT
