Dr Steinbrecher,
While I was going through the analysis of removal of vdW parameters using
soft-core potentials, the dV/dL values deviate much more in the range of
0.4-0.6. It happens in your JCC manuscript too. Its for Chloride ion Fig 6b.
Further, I did another calculation for the KCl in water.
I followed the similar protocol as your A9 tutorial.
The system preparation is as follows:
V0
K+ Cl- and H2O
V1
H2O
The Coulomb part is smooth, but when I come to the vander Waals part at
lambda = 0.96. 0.97, 0.98, 0.99, the deviations of dV/dL are really very
large and the associated rms in dV/dL is large too.
Below are the values pasted from my step2 (removal of VdW) for KCl in water.
lambda dV/dL rms
0.01 -10.1308 7.6823
0.02 -10.3832 7.8315
0.03 -10.5346 7.7157
0.04 -11.1133 8.4021
0.05 -11.0010 8.3304
0.10 -11.8918 8.9928
0.15 -15.8839 13.8790
0.20 -21.5457 12.5220
0.25 -19.6375 7.7632
0.30 -16.7392 5.8578
0.35 -13.6715 5.5840
0.40 -12.1145 5.8446
0.45 -11.4377 6.5548
0.50 -14.9366 9.3140
0.55 -17.6222 9.2010
0.60 -19.6371 7.3480
0.65 -17.6970 5.5395
0.70 -16.0031 4.8710
0.75 -14.8000 4.6733
0.80 -14.3021 5.5109
0.85 -15.6648 7.1867
0.90 -19.9225 10.2446
0.95 -36.7524 20.6859
0.96 -45.3181 25.7754
0.97 -60.0310 34.3345
0.98 -89.1323 51.1157
0.99 -177.6619 106.7890
When I plotted the temperature, density, Etot, EPtot, all are well behaved
and do not show any abnormal deviations.
Is there anything that I'm missing in my simulations?
I can provide more details if necessary.
Thank you very much for your time.
Regards
Sai
On Fri, Jan 13, 2012 at 7:28 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > I used the following protocol from the example in tutorial A9.
>
> Thats looks fine to me.
>
> > Since I dont have any atoms or charges to be added, I dont have step3. Am
> > I right in assuming this?
>
> yes, in this case that third step would be unneccesary.
>
> > The values are close to your JCC paper titled "Soft-core Potentials in
> ...
> > Further, my values are shifted in sign for step 1 and step 2.
> > Am I doing something wrong here?
>
> Well, if you reproduce our values, then everything should be correct.
> TIP3P vs. TIP4PEw may make a small difference. The sign comes from the
> fact that you are simulating the removal of Cl- from water, while in our
> paper we report solvation free energies, which correspond to the reverse
> process. My raw numbers had the same signs as yours.
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Wed Jan 18 2012 - 10:00:03 PST
