[gmx-users] zero charge model- simulation time

[Justin A. Lemkul]

Juliette N. wrote:
> Hi again,
> 
> I am wondering if using tpbconv to set zero charges (case 1) works 
> similar to when one sets zero atom charges in topology file from the 
> very beginning (case 2). Do these two cases work similarly?
> 

They should work identically.

> I checked tpr file and I see that charges are set to zero.
> 
> Can you please tell me what these lines mean?
> 
> Does it refer to exclusion which is set to 3 in top file?
> 

Yes.

> excls[0][0..10]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10}
>          excls[1][11..18]={0, 1, 2, 3, 4, 5, 6, 7}
> 
> The number of these lines corresponds to atom numbers in the system.
> 

They refer to the atom indices of the atoms in the [moleculetype], not the 
consecutive numbering of the system (for the first molecule this will be the 
same, but I thought I'd point that out).

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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