Dear Prof. Case:
Thank you very much, I did a separate run, the curve in all
three steps are smooth and no singularity.
There are net charge in softcore region, the absolute value of dvdl I
got in electrostatics is about one order of magnitude larger than vdW.
I think this may be the reason that I got a strange curve in one-step
run.
ps. I suggest that Amber main page give out a ris file of citation
info which can be imported to Endnote easily.
Best Regards!
Denis
2012/8/14 David A Case <case.biomaps.rutgers.edu>:
> 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 - 19:00:04 PDT
