[gmx-users] itp atomtypes section

[Tsjerk Wassenaar]

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