Subashini .K subashinik at hotmail.com
Sat Mar 4 15:24:39 CET 2017

Hi gromacs users,

I want to calculate delta G for protein ligand binding.

Had run the umbrella pulling simulation   for 100 ps (protein ligand solvated in water), applying restraint in the protein (using the code in gromacs tutorial website, Bevenlab).

But, after running the perl script  (perl distances.pl), did not obtain any distance on the right column (summary_distances.dat). It was blank.

(1) Had applied the position restrain of the protein during NPT equilibration.

(2) During puling simulation, again applied the restrain on the protein. Is it correct?

How to rectify the mistake and proceed in the right direction?



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