So, I also check the literature, for water, using flexible SPC model, in Buckingham potential form........ How do I use the Buckingham potential form for flexible SPC model? rewriting the itp for water?
Best XJ 在 2011年11月15日 下午12:12，xiaojing gong <[email protected]>写道： > Many thanks > > > 2011/11/15 Mark Abraham <[email protected]> > >> On 15/11/2011 9:17 PM, xiaojing gong wrote: >> >> .......I am not sure.......Do you have some suggestions? >> >> >> No. The two functional forms are incompatible. GROMACS only allows you to >> define one set of nonbonded parameters, so you can only use one functional >> form in a given simulation. This is fixed in the [defaults] section. I >> suggest you go and look at how the literature models CNT plus water. >> >> Mark >> >> >> >> 在 2011年11月15日 上午11:05，Mark Abraham <[email protected]>写 道： >> >>> On 15/11/2011 9:03 PM, xiaojing gong wrote: >>> >>> Many thanks for reply. >>> Another question, If I use Buckingham potential for CNT, and I want to >>> simulate CNT and water, shall I also transfer the SPC.itp from LJ to >>> Buckingham potential? >>> >>> The most important is how to transfer? >>> I will appreciate it if you can give me any suggestions. >>> >>> >>> How would you compute VDW interactions between carbon atoms and water >>> atoms? >>> >>> Mark >>> >>> >>> >>> Best >>> XJ >>> >>> 2011/11/14 Mark Abraham <[email protected]> >>> >>>> On 15/11/2011 2:00 AM, xiaojing gong wrote: >>>> >>>>> Hi dear all, >>>>> For Buckingham potential， there is three parameters A B C >>>>> In GMX, the units of A B C is the kJ/mol, nm, kJ/mol*nm^6， am I right? >>>>> >>>> >>>> Manual section 2.2 defines the units, and 4.1.2 defines the >>>> functional form. >>>> >>>> Mark >>>> -- >>>> gmx-users mailing list [email protected] >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>>> >>> >>> >>> >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >> >> >> >> >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> > >
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
