[gmx-users] Error in -rerun

Apramita Chand apramita.chand at gmail.com
Fri Jun 15 13:11:07 CEST 2018

Dear All,
As I have specified in my earlier mail, I wanted to know which input
trajectory has to be supplied to -rerun flag in mdrun for recalculation of
electrostatic energies between protein-solvent from gromacs (as proposed by
Lindgren et al, in the paper "On the stability of chymotrypsin inhibitor 2
in a 10 M urea solution. The role of interaction energies for urea-induced
protein denaturation",)

As I was confused about the input files, I am doing a trial where I am
supplying the production run trajectory to -rerun.
This involves making changes in the cut-offs and applying cut-off scheme
rather than PME.

My cubic box length is 3.20 and I cannot specify any cutoffs exceeding half
of this length,(without changing the box length). So I apply whatever
cut-offs are possible with my present box size.

I am getting the error:

*Rerun trajectory frame step 0 time 0.000000 has too small box dimensions*

after running mdrun

Please help me troubleshoot the issue

Thanking you,
Yours sincerely,
Apramita Chand

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