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
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