[gmx-users] itp atomtypes section
tsjerkw at gmail.com
Tue Nov 27 09:25:03 CET 2012
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,
On Tue, Nov 27, 2012 at 3:45 AM, James Cannon <jamesresearching at gmail.com>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
> [ 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,
> gmx-users mailing list gmx-users at gromacs.org
> * 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 gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Tsjerk A. Wassenaar, Ph.D.
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
More information about the gromacs.org_gmx-users