Tanping Li wrote:
Dear David,
Thank you so much for the reply. I used the pme,
cutoff for rvdw =1.4, rlist=rcoulomb=0.9, so that is
not supposed to give me the same rotational relaxation
time for SPC/E as 3.8ps in your paper?
No. If you want to reproduce literature you have to do it exactly the
same way.
Best
Tanping
--- David van der Spoel <[EMAIL PROTECTED]> wrote:
Tanping Li wrote:
Dear all,
I simulated a box of pure water usin NPT. I use
gmx96
force field and standard mdp file for the gmx96
force
field. The time scale of dipole correlation
function
is 2.8ps, which is different from David's result
3.8ps
in the JCP paper. Is this 3.8ps sensitive to the
mdp
file or the force field? I just wonder if there is
a
bug in my program. I tried a lot, but still can't
get
3.8ps. Really appretiate your idea, I have
struggled
for this for a long time.
You need to use *exactly* the same parameters to
reproduce it, in
particular cutoffs and reaction field, dispersion
correction and so on.
Yours
Tanping
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________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular
Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala
University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED]
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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