[gmx-users] zero charge model- simulation time

Juliette N. joojoojooon at gmail.com
Thu Jul 28 20:22:48 CEST 2011

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?

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?

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.

Thank you so much,
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