Dear David:
Thank you so much for the valuable information.
Our conclusion in the above paper is to use PME for Coulomb and not shift
Van der Waals
I have read the paper you mentioned and did not find how you treated the
VdW. Have you done some work on the cut off method for vdw? Since I used
Dear all:
This is the mdp I just used for the system. The funny thing is after a 8ns
simulation I got a very high pressure and temperature:
Temperature 343.437
Pressure (bar) 45.782
I also did another run with removing the vdw_switch in mdp and keep all
other
Yanmei Song wrote:
Dear all:
This is the mdp I just used for the system. The funny thing is after a
8ns simulation I got a very high pressure and temperature:
Temperature 343.437
Pressure (bar) 45.782
I also did another run with removing the vdw_switch in
Dear All:
I found when I changed the vdwtype from cut-off to shift, the density of the
system decrease significantly.All the other setting in the mdp file remain
unchanged. For example the density of TIP5P water drops to 962. Does it mean
I can not use the shift for vdwtype?
--
Yanmei Song
Yanmei Song wrote:
Dear All:
I found when I changed the vdwtype from cut-off to shift, the density of
the system decrease significantly.All the other setting in the mdp file
remain unchanged. For example the density of TIP5P water drops to 962.
Does it mean I can not use the shift for
Dear Mark:
Thanks for your answer. I have to use the same mdp file for both water and
another polymer molecules in my system, right? Then if the shift function
works well for the polymer, I can not get the best result for TIP5P? The
density of TIP5P is different from the literature value of
Yanmei Song wrote:
Dear Mark:
Thanks for your answer. I have to use the same mdp file for both water
and another polymer molecules in my system, right? Then if the shift
function works well for the polymer, I can not get the best result for
TIP5P? The density of TIP5P is different from
Dear Justin:
Yes. Before I do the water+polymer, I did both the bulk systems separately.
The density of TIP5P I mentioned earlier is the results for pure water bulk
system. My concern is that if it is reasonable that the property of the
system changes with different mdp conditions? Since when I
Yanmei Song wrote:
Dear Justin:
Yes. Before I do the water+polymer, I did both the bulk systems
separately. The density of TIP5P I mentioned earlier is the results for
pure water bulk system. My concern is that if it is reasonable that the
property of the system changes with different mdp
Dear Justin:
Yes and I tried dispersion correction and it gives a larger density than I
expected. The density of the polymer by vdwtype=shift is more close to the
experimental value. Then your suggestion would be to choose the
vdwtype=cut-off under this condition even if it result in larger
Yanmei Song wrote:
Dear Justin:
Yes and I tried dispersion correction and it gives a larger density than
I expected. The density of the polymer by vdwtype=shift is more close
to the experimental value. Then your suggestion would be to choose the
vdwtype=cut-off under this condition even
Perhaps I can contribute something else that might be a bit more useful. It
just occurred to me that if you are only changing the vdwtype parameter, then
you are not correctly implementing the shift function. See here for proper use
of a shift potential:
Dear Justin:
Thanks so much for your effort and information. Perhaps I did not set the
proper value for vdw_switch. I will try some value. I really appreciate your
nice help!
On Mon, May 18, 2009 at 5:24 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Perhaps I can contribute something else that
Justin A. Lemkul wrote:
Yanmei Song wrote:
Dear Justin:
Yes and I tried dispersion correction and it gives a larger density
than I expected. The density of the polymer by vdwtype=shift is more
close to the experimental value. Then your suggestion would be to
choose the vdwtype=cut-off
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