[gmx-users] martian thing

Miguel Ángel Mompeán García mig.mompean at gmail.com
Tue Oct 30 12:06:35 CET 2012

Dear gmx users,

Something very weird is happening with a .gro file and I wonder if any user
has ever experienced something similar...

I am doing umbrella sampling simulation on a peptide with capped termini
residues (ACE and NH2). As starting structure for the pulling simulations I
used the last frame from a 150 ns simulation, in order to asses the
stability of my system before the umbrella procedure.
I did NVT and NPT equilibration, and then the MD run.
Then I extracted the last frame of that 150 ns run and placed it into an
appropriate box for the pulling, so I run again editconf, genbox and energy
minimization. Then at the equilibration step the weird thing came: in the
.gro file I have the ACE residues written as NH2 in one of the chains! The
atom names remain as they have to according to the force field nomenclature
(CH3, HH31, HH32, ...) for this ACE of this chain, but it is name as NH2!!!

This is happening only in this .gro file at this step. Everything is fine
in the first equilibrations, the MD run, the energy minimization in the
newbox... It just shows up after this equilibration.

I wonder if I may just change NH2 to ACE where it is to be or it has to be
with something more complicated.

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