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 density? Thank you so much!
On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > 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 >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- Yanmei Song >> Ph.D. Candidate >> Department of Chemical Engineering >> Arizona State University >> >> >> >> ------------------------------------------------------------------------ >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search >> before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> 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 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> 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 > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php