[gmx-users] energy of each residue??

Pradeep Kota kotanmd at gmail.com
Tue May 1 13:46:19 CEST 2007

Dear users,

I'm trying to compute the contribution of each residue to the total energy
of a protein. I neutralized my system with 8 chloride ions and then made an
index file with each residue in a different index group, using 'splitres'
via make_ndx. it gave me an index file with atoms of each residue in
different index groups. but as all these atoms are again listed in the
default index group - Protein, grompp shouts out a fatal error. there was a
post on the list about index groups being bungled up after taking the system
thro genion. but i dont think genion really matters in my case. any inputs?
my idea is to calculate the energy of each residue in a given protein. i
wish to run a simulation for 10 ps for that. am i going wrong anywhere? is
there a better way?

thanks in advance
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