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 the literature value of
982. Thanks!
So your system is water + polymer? In that case, you have an added variable -
the interaction between the water and your polymer. What you should probably be
more concerned with the what the bulk density of the whole system is. I have
found that analyzing densities of portions of mixed systems does not give an
accurate result.
-Justin
On Mon, May 18, 2009 at 3:33 PM, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
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 vdwtype?
Maybe not. Check out the paper in which TIP5P was parameterized. The
greater the extent to which your .mdp conditions differ from those
conditions, the greater the likelihood that the parameterization is
no longer valid.
Mark
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Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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