Dear Justin:<br><br>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 density? Thank you so much!<br>
<br><div class="gmail_quote">On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Yanmei Song wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Justin:<br>
<br>
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?<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Yanmei Song wrote:<br>
<br>
Dear Mark:<br>
<br>
Thanks for your answer. I have to use the same mdp file for both<br>
water and another polymer molecules in my system, right? Then<br>
if the shift function works well for the polymer, I can not get<br>
the best result for TIP5P? The density of TIP5P is different<br>
from the literature value of 982. Thanks!<br>
<br>
<br>
So your system is water + polymer? In that case, you have an added<br>
variable - the interaction between the water and your polymer. What<br>
you should probably be more concerned with the what the bulk density<br>
of the whole system is. I have found that analyzing densities of<br>
portions of mixed systems does not give an accurate result.<br>
<br>
-Justin<br>
<br>
<br>
On Mon, May 18, 2009 at 3:33 PM, Mark Abraham<br>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>> wrote:<br>
<br>
Yanmei Song wrote:<br>
<br>
Dear All:<br>
<br>
I found when I changed the vdwtype from cut-off to shift, the<br>
density of the system decrease significantly.All the other<br>
setting in the mdp file remain unchanged. For example the<br>
density of TIP5P water drops to 962. Does it mean I can<br>
not use<br>
the shift for vdwtype?<br>
<br>
<br>
Maybe not. Check out the paper in which TIP5P was<br>
parameterized. The<br>
greater the extent to which your .mdp conditions differ from<br>
those<br>
conditions, the greater the likelihood that the<br>
parameterization is<br>
no longer valid.<br>
<br>
Mark<br>
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Arizona State University<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
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Ph.D. Candidate<br>
Department of Chemical Engineering<br>
Arizona State University<br>
</div></blockquote>
<br>
-- <br><div><div></div><div class="h5">
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Yanmei Song<br>Ph.D. Candidate<br>Department of Chemical Engineering<br>Arizona State University<br>