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
