Dear Justin: Thanks so much for your effort and information. Perhaps I did not set the proper value for vdw_switch. I will try some value. I really appreciate your nice help!
On Mon, May 18, 2009 at 5:24 PM, Justin A. Lemkul <[email protected]> wrote: > > Perhaps I can contribute something else that might be a bit more useful. > It just occurred to me that if you are only changing the vdwtype parameter, > then you are not correctly implementing the shift function. See here for > proper use of a shift potential: > > http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html#vdw > > Take note of the necessary changes to vdw_shift, and potentially rlist. A > few quick tests of the shift function indicate the following: > > Case 1. Plain cutoff's at 1.2 nm > Density: 988 kg/m^3 > > Case 2. Shift potential (no other changes, i.e. rvdw_switch = 0, rvdw = > 1.2) > Density: 962 kg/m^3 > > Case 3. More appropriate shift potential (rvdw_switch = 1.0, rvdw = 1.2) > Density: 983 kg/m^3 > > -Justin > > > Justin A. Lemkul wrote: > >> >> >> Yanmei Song wrote: >> >>> 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! >>> >>> >> 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. >> >> -Justin >> >> On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul <[email protected]<mailto: >>> [email protected]>> 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 >>> <[email protected] <mailto:[email protected]> >>> <mailto:[email protected] <mailto:[email protected]>>> 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 >>> <[email protected] <mailto:[email protected]> >>> <mailto:[email protected] <mailto:[email protected]>> >>> <mailto:[email protected] >>> <mailto:[email protected]> >>> <mailto:[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 >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> <mailto:[email protected]> >>> <mailto:[email protected] <mailto: >>> [email protected]>> >>> <mailto:[email protected] >>> <mailto:[email protected]> <mailto:[email protected] >>> <mailto:[email protected]>>> >>> >>> >>> 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 [email protected] >>> <mailto:[email protected]> >>> <mailto:[email protected] >>> <mailto:[email protected]>> >>> <mailto:[email protected] >>> <mailto:[email protected]> >>> <mailto:[email protected] >>> <mailto:[email protected]>>>. >>> >>> 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 [email protected] >>> <mailto:[email protected]> >>> <mailto:[email protected] <mailto: >>> [email protected]>> >>> 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 [email protected] >>> <mailto:[email protected]> >>> <mailto:[email protected] >>> <mailto:[email protected]>>. >>> 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> <http://vt.edu> | (540) >>> 231-9080 >>> >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> <mailto:[email protected]> >>> <mailto:[email protected] <mailto:[email protected]>> >>> 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 [email protected] >>> <mailto:[email protected]> >>> <mailto:[email protected] >>> <mailto:[email protected]>>. >>> 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 <http://vt.edu> | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> <mailto:[email protected]> >>> 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 [email protected] >>> <mailto:[email protected]>. >>> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University
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