Dear David:<br><br>Thank you so much for the valuable information.<br><br> "Our conclusion in the above paper is to use PME for Coulomb and not shift Van der Waals"<br><br>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 PME for Coulomb in my system. I am still confusing why not shift for vdw. <br>
<br>" I would also recommend to use TIP4P rather than
TIP5P, as Jorgensen uses TIP4P for all his parameterizations."<br><br>I have read Jorgensen's paper for the OPLS and realized that the TIP4P would be the first choice for combining with OPLS. However my concern is that TIP4P model is not as good as TIP5P in terms of diffusion constant and viscosity which are extremely important for my purpose. <br>
<br>I also have compared SPC and TIP4P and turn out that SPC can give a better result for my system. Unfornately SPC has a very bad viscosity as TIP4P. So I am trying TIP5P.<br><br>Do you think OPLS+ TIP5P can cause serious problem or horrible artifacts. If you can suggest some literatures on this that would be great.<br>
<br>I really appericate all your help! <br><br><div class="gmail_quote">On Mon, May 18, 2009 at 10:37 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</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;">Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<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><div>
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></blockquote><div>
<br>
No. My suggestion is to do your homework, as Mark originally said, and as I echoed in my last mail. Read about the water model, its expected performance under different simulation parameters, and evaluate what you want to do once you have done this background work. If you have done a thorough literature review, there is no one else that can make a choice for you; decide how to handle your system based on what you read.<br>
<br>
</div></blockquote>
Actually this is not so easy. Jorgensen has never published the way he treats cut-offs, but he was friendly enough to let me know, so we have actually done it:<br>
David van der Spoel and Paul J. van Maaren: The origin of layer structure artifacts in simulation of liquid water J. Chem. Theor. Comp. 2 pp. 1-11 (2006)<br>
<br>
If you look in the appendix you can find the "one and only" </blockquote><div> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
OPLS. However!!!! This is not to be recommended since the effect is very different for MD and MC (what Jorgensen uses). In MD the official method will give horrible artifacts. In other words, you have to use something better. Our conclusion in the above paper is to use PME for Coulomb and not shift Van der Waals. I would also recommend to use TIP4P rather than TIP5P, as Jorgensen uses TIP4P for all his parameterizations.<div>
<div></div><div><br>
<br>
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
-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;">
On Mon, May 18, 2009 at 4:29 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 Justin:<br>
<br>
Yes. Before I do the water+polymer, I did both the bulk systems<br>
separately. The density of TIP5P I mentioned earlier is the<br>
results for pure water bulk system. My concern is that if it is<br>
reasonable that the property of the system changes with<br>
different mdp conditions? Since when I did the bulk water and<br>
bulk polymer system, I found the densities change with different<br>
cutoff and vdwtype conditions. Is this a artifact? Or the larger<br>
cutoff, the more accurate result we can get?<br>
<br>
<br>
Every parameter you specify will affect the results you see. I<br>
agree with Mark - look up the original reference for TIP5P and see<br>
what parameters are recommended. Also read the subsequent<br>
literature that has used TIP5P to see what modifications<br>
(electrostatic treatment, vdW treatment, etc) are appropriate or<br>
even more accurate.<br>
<br>
Also realize that using vdwtype = shift may not be the best<br>
solution. I only suggested as a guess for something to try back<br>
when you were getting bizarre results with your polymer. Have you<br>
ever tried dispersion correction when using vdwtype = cutoff? I<br>
routinely use such a setup and have never seen any really bizarre<br>
behavior.<br>
<br>
-Justin<br>
<br>
On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul<br>
<<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>><br>
<mailto:<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<br>
for both<br>
water and another polymer molecules in my system, right?<br>
Then<br>
if the shift function works well for the polymer, I can<br>
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<br>
added<br>
variable - the interaction between the water and your<br>
polymer. What<br>
you should probably be more concerned with the what the bulk<br>
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> <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>><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<br>
shift, the<br>
density of the system decrease significantly.All<br>
the other<br>
setting in the mdp file remain unchanged. For<br>
example the<br>
density of TIP5P water drops to 962. Does it mean<br>
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<br>
differ from<br>
those<br>
conditions, the greater the likelihood that the<br>
parameterization is<br>
no longer valid.<br>
<br>
Mark<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>>><br>
<br>
<br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list.<br>
Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>>>.<br>
<br>
Can't post? Read<br>
<a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
<br>
<br>
-- Yanmei Song<br>
Ph.D. Candidate<br>
Department of Chemical Engineering<br>
Arizona State University<br>
<br>
<br>
------------------------------------------------------------------------<br>
<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>>.<br>
Can't post? Read<br>
<a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
-- ========================================<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> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<br>
231-9080<br>
<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
<br>
<br>
-- Yanmei Song<br>
Ph.D. Candidate<br>
Department of Chemical Engineering<br>
Arizona State University<br>
<br>
<br>
-- ========================================<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> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
<br>
<br>
-- <br>
Yanmei Song<br>
Ph.D. Candidate<br>
Department of Chemical Engineering<br>
Arizona State University<br>
</blockquote>
<br>
</blockquote>
<br>
<br>
-- <br></div></div><font color="#888888">
David van der Spoel, Ph.D., Professor of Biology<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a></font><div>
<div></div><div><br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</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>