[gmx-users] POPC simulation with heavy hydrogens and 4 fs timestep

Ganesh Shahane ganesh7shahane at gmail.com
Thu Nov 19 13:49:07 CET 2015

Dear Gromacs Users,

I have been trying to simulate a pure POPC bilayer with a timestep of 4 fs
and heavy hydrogens, using the charmm36 ff. Towards this end, I constructed
the bilayer using Charmm-GUI and used pdb2gmx with the -heavyh flag to
generate the appropriate topology.

However when I use the grompp to generate the .tpr file, I get a warning:
"Overriding atomtype OT". A quick look in the Charmm36 ffnonbonded.itp
revealed that the atomtype OT corresponds to an oxygen with reduced atomic
mass, which is perfectly understandable given the use of -heavyh flag.

My problem is that I don't understand what the warning exactly means. A
look at a previous gromacs thread where this "overriding atomtype" problem
has been reported, didn't help.

Is it safe to ignore this warning?

When I ignored the warning and carried out a simple NVE run, it gave me
potential, kinetic and total energies that were not conserved. Please find
the plot of the energies and the associated NVE run parameters at this link
A look at the trajectory in VMD revealed that the molecules which were
initially very dynamic, start "freezing" as the KE approaches zero.

Does anybody has any idea as to where I am going wrong?

Thank you.

Best Regards,
Ganesh Shahane

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