[gmx-users] Gro file does not match topology file... continue

Tasneem Kausar tasneemkausar12 at gmail.com
Sat Jan 28 02:39:55 CET 2017

Yes , you are right. I was also surprised that when atoms in gro and
topology match then how this error can be.
In my case I was simulating a small peptide segment in water. Everything
goes smoothly in it. Then I have generated a system with 8 peptides using
genconf command.
I have generated a box with editconf with -d 1.1 in a cubical box. In last
line of topology file protein_chain_A was changed from 1 to 8. The genbox
was used to solvate the system. Then grompp gives  the mismatch error.
Then with a box size of 2.1grompp was executed without any error.
Same mdp file was used in both the case.

This is the whole procedure, I have followed.

This is why I was saying to increase the box size.


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