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 conditions? Since when
I did the bulk water and bulk polymer system, I found the densities
change with different cutoff and vdwtype conditions. Is this a artifact?
Or the larger cutoff, the more accurate result we can get?
Every parameter you specify will affect the results you see. I agree with Mark
- look up the original reference for TIP5P and see what parameters are
recommended. Also read the subsequent literature that has used TIP5P to see
what modifications (electrostatic treatment, vdW treatment, etc) are appropriate
or even more accurate.
Also realize that using vdwtype = shift may not be the best solution. I only
suggested as a guess for something to try back when you were getting bizarre
results with your polymer. Have you ever tried dispersion correction when using
vdwtype = cutoff? I routinely use such a setup and have never seen any really
bizarre behavior.
-Justin
On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>> 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 <http://vt.edu> | (540) 231-9080
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--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
--
========================================
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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