[gmx-users] WHAT TO DO WITH BAD CONTACTS?

[radhika jaswal]

Hi  all,

I did a simulation of unusual protein in pure methanol for 1 ns but in
final results there was a bad contact of methanol molecule (no. 508)
with carbonyl oxygen of the acetyl group of  the N terminal. I was
trying to remove this particular molecule and wanted to extend the run
but same problem of character coding of .trr and .tpr file. But I do
not want to start the fresh run of 1 ns because other methanol molecule
will take its place. In extending of run there is need of these two
files. Looking for suggestions.

With lot of Thanks






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