[gmx-users] itp atomtypes section

[James Cannon]

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 <tsjerkw at gmail.com> 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 <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
> > 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
> > --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Biocomputing Group
> Department of Biological Sciences
> 2500 University Drive NW
> Calgary, AB T2N 1N4
> Canada
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