[gmx-users] Using tpbconv_d -zeroq

יוכבד ybaime at gmail.com
Tue Feb 21 15:08:46 CET 2012


I ran a md simulation for a system with two groups: Surrounding , LIG.
I wish to set the charges of the surrounding group to zero and to
recalculate the Coulomb interactions between the groups.
For this purpose I used tpbconv  with the -zeroq option:

tpbconv_d -s md_prev.tpr -f md_prev.trr -n -o md_new.tpr -zeroq
and I selected the surrounding group as the group that will be "zeroed".

next I ran a rerun:

mdrun_d -nt 8 -v -deffnm md_new -rerun md_prev.xtc

after the rerun finished I used g_energy to analyze the results:

 g_energy_d -f md_new.edr -o md_new.xvg

The Coul-SR:Surrounding-Surrounding was 0 as expected and so was
the problem is that also Coul-SR:LIG-LIG was also 0 (and the same for the
LR values).
Could anyone please help me understand why this happened?

Thank you very much
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