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!
On Mon, May 18, 2009 at 3:33 PM, Mark Abraham <[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] > 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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