Nick wrote:
One last question!
1- So what are the 12 energy terms I get by passing index file onto step
2 below? I ignored rerun! what does rerun does?
I don't know what 12 terms you're referring to. You'll get A-A, A-B, and B-B
short-range nonbonded terms, the exact enumeration of wh
One last question!
1- So what are the 12 energy terms I get by passing index file onto step 2
below? I ignored rerun! what does rerun does?
2- So I dont have to include index file in mdrun initially..In brief what I
need is:
step 1 grompp .(no index)
step 2 mdrun -s old.tpr
Nick wrote:
Dear Justin,
Thanks for your reply and Sorry for asking naive questions...
1- I am looking at all possible interaction energies between components
A and B. that is A-A AB and BB. So interaction between single chains is
not what I want. With this I think my initial approach was
Dear Justin,
Thanks for your reply and Sorry for asking naive questions...
1- I am looking at all possible interaction energies between components A
and B. that is A-A AB and BB. So interaction between single chains is not
what I want. With this I think my initial approach was right. That is
putt
Nick wrote:
Dear experts,
1- I am trying to get interaction energies between solute (3 chains A)
and solvent 50 molecules B. In the index file I created two groups: one
for all atoms of [A] and and [B] for all solvent molecules. and by
setting A and B as energy groups in mdp file I am getti
Dear experts,
1- I am trying to get interaction energies between solute (3 chains A) and
solvent 50 molecules B. In the index file I created two groups: one for all
atoms of [A] and and [B] for all solvent molecules. and by setting A and B
as energy groups in mdp file I am getting break down as A-
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