[gmx-users] problem with simulation of phosphatidic acid, possibly in my topology?

[Mark Abraham]

himanshu khandelia wrote:
> Hi,
> 
> I am trying to run a simulation of a POPC bilayer mixed with some
> mono-anionic Phosphatidic acid (POPA) , where the choline group is
> replaced by a hydrogen atom. However, the energy of my simulation box
> diverges, and I am trying to fix the problem. I also tried running a
> simulation of PA solvated in water and a single sodium ion, but even
> that does not work. I will try to provide as much detail as possible,
> I hope someone can help point out some obvious error which I have not
> been able to debug over 3 days. In the simulation of a single PA
> molecule in water, MDRUN keeps complaining that the distance between
> atoms H1 and O4 is very high (> 4 nm or so). The problem probably lies
> in my topology, possibly in the bonded interactions?

Merely replacing a functional group with a hydrogen doesn't make for a 
sensible model physics. First, you probably didn't conserve charge, and 
second the parameters don't necessarily make sense for a particle of 
mass 1 rather than mass 12 (plus secondary effect of substituent group), 
and third there's no way to fix both the foregoing and the other issues.

You need at least to find a proper model of POPA and to implement it, or 
if need be, develop one yourself. Search the wiki for Parameterization 
to get a start on the latter, but it is an expert topic.

Mark