On Sun, Aug 12, 2012, Liu Denis wrote:
> Is the vdW-radii and solvated charges defined in prmtop file? If
> so, there should not be change outside the scmask. In fact, I did a
> null transform, namely use the identical prmtop and inpcrd file for
> both V0 and V1, steep slope was still seen at the two end of the
> curve.
> I attached my prmtop, input, part of output file at lambda=0.01
> after 1ns production run of the null transform in the email. Could you
> help me to find out what
> is wrong in it?
>
> 0.01 37.10
> 0.05 13.47
> 0.10 -1.23
> 0.15 -7.53
> 0.20 -11.12
> 0.25 -12.42
> 0.30 -12.45
> 0.35 -10.70
> 0.40 -8.23
> 0.45 -4.52
> 0.50 0.00
> 0.55 4.66
> 0.60 8.41
> 0.65 10.70
> 0.70 12.05
> 0.75 12.37
> 0.80 11.11
> 0.85 7.79
> 0.90 0.80
> 0.95 -13.16
> 0.99 -37.61
Your "null transform" appears to give close to zero in free energy, so that is
good. And the curve looks very smooth, which is also good. I'd suggest
trying separately decoupling the electrostatics and the vdW terms. Also,
figure out the net charge in the softcore region: if this is non-zero, that
might help explain some of the shape you are seeing.
Right now, Dr. Steinbrecher is on vacation, so you might have to wait a couple
of weeks for his input here.
...dac
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Received on Tue Aug 14 2012 - 05:30:05 PDT
