Dear Tsjerk, Thanks for clarifying that for me. I appreciate it.
Best regards, James On Tue, Nov 27, 2012 at 5:25 PM, Tsjerk Wassenaar <[email protected]> wrote: > Hi James, > > The 6 and 1 are the number of electrons the atomtype has, which is used for > QM/MM stuff. Gromacs can tell whether or not it is given by checking the > format of the line. If the 5th column is a letter, then the number isn't > there, if the 6th column is a letter, it must be there. > > Hope it helps, > > Tsjerk > > > On Tue, Nov 27, 2012 at 3:45 AM, James Cannon <[email protected] > >wrote: > > > Dear users, > > > > I apologise if this is a stupid question, however after a morning of > > searching I have not been able to find the answer. > > > > 1. I have a sample itp file and it contains a section like this: > > [ atomtypes ] > > CF CF 6 12.01100 0.2588 A 3.50000e-01 2.56134e-01 > > HF HF 1 1.00800 0.1000 A 3.50000e-01 4.28529e-01 > > > > I can't work out what the column containing the "6" and "1" is for. Can > > anyone help? It's not documented anywhere that I can find. > > > > > > > > 2. I notice that there are many types of "atomtypes" fields. From the > > manual: > > [ atomtypes ] > > ;name mass charge ptype c6 c12 > > O 15.99940 0.000 A 0.22617E-02 0.74158E-06 > > OM 15.99940 0.000 A 0.22617E-02 0.74158E-06 > > > > This is clearly a different format to my sample above. Why does the > format > > vary? I know the above format is not wrong because it runs succcessfully > in > > a test-run. How does gromacs know which format to use correctly? > > > > I appreciate any help. > > Thank you. > > Best regards, > > > > James > > -- > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Biocomputing Group > Department of Biological Sciences > 2500 University Drive NW > Calgary, AB T2N 1N4 > Canada > -- > 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
