Dear David, Thank you so much for your reply! I did try to use nstlist = -1 and I still cannot solve the energy drifting problem. And you can see my problem in more detail from the following link: http://lists.gromacs.org/pipermail/gmx-users/2009-December/047299.html
And you mentioned I should use shifted VDW. But in the way I use tabulated potential, the option in vdwtype should be User so that I can indicate I am using a lookup table for the tabulated potential. (In my test case, I used the table provide by GMX 4.0.5 /share/gromacs/top/table6-12.xvg directly, and just changed its name to be table.xvg.) So it seems to me there is no explicit way I can use shift function. Or should I shift the function by changing the potential in the table? Thanks again for your help. Zhe On Tue, Dec 8, 2009 at 1:38 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > Zhe Wu wrote: >> >> I agree with that. But I don't know why, when using tabulated >> potential, I cannot even get a box of LJ particles to have energy >> conservation in NVE. Anyone has some idea? >> > > do you use shifted VdW and nstlist = 1 or nstlist = -1? >> >> Zhe >> >> On Tue, Dec 8, 2009 at 3:52 AM, XAvier Periole <x.peri...@rug.nl> wrote: >> >>> >>> One solution would be to use tabulated potential for which the >>> analytical form does not matter. >>> >>> On Dec 8, 2009, at 4:29 AM, Mark Abraham wrote: >>> >>> >>>> >>>> hong bingbing wrote: >>>> >>>>> >>>>> Dear all, >>>>> Has anyone tried to use 2 van de Waals interaction types in one system? >>>>> For example, the system includes two components A and B. The van de >>>>> Waas >>>>> interaction for A is LJ type, while for B Buckingham form is used. Can >>>>> GROMACS support two forms simultaneously? >>>>> >>>> >>>> No. How would you describe the vdW interaction between an atom from A >>>> and >>>> one from B? >>>> >>>> If the reason for this question is based on a desire to mix two force >>>> fields - don't. >>>> >>>> Mark >>>> -- >>>> gmx-users mailing list gmx-us...@gromacs.org >>>> http://lists.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 >>>> >>> >>> -- >>> gmx-users mailing list gmx-us...@gromacs.org >>> http://lists.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 thewww >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Professor of Biology > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > sp...@xray.bmc.uu.se sp...@gromacs.org http://xray.bmc.uu.se/~spoel > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.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 > -- gmx-users mailing list gmx-users@gromacs.org http://lists.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
