Dear Maria,
I am not sure but something you should look further is the rotation
around your P3-O2 bond (which is P8-O7 in Tieleman's topology).
It is described by the first two lines of your dihedral section
topology:
1 2 3 6 1 0.0 1.05 3
1 2 3 6 1 0.0 3.14 2
which I see you took identical to the corresponding lines of Tieleman.
But in your case this is a rotation around O-P-O-H and in POPC it's
around O-P-O-C
I would expect that the function fitting these two dihedrals changes
between POPC and POPA.
Probably the P-O-H angle should also differ from the P-O-C and that
could have an influence on the other angles around P.
These two parts of the topology are I believe to be verified.
Ioannis
Le 5 mai 08 à 15:53, maria goranovic a écrit :
Dear Mark,
Sorry, perhaps I should have clarified more. I did not just make a
blind substitution of a choline by a H-atom.
First, I did conserve charge.
Second, I did introduce reasonable non-bonded and bonded interaction
parameters for the new H-atom. The non-bonded interaction parameters
were similar to those suggested by the mono-anionic phosphate group
on a threonine or serine.
I guess you will agree force fields are often set up that entire
functional groups from one molecule can be transferred to others.
For example, one can use the same head group for both POPC and DPPC,
or conversely, one can use different types of hydrocarbon chains for
the same head group, from 12 carbons to 20 carbons, as has often
been done. The only parameters that might change in getting POPA
from POPC are near the H-atom itself, and those are the ones that I
had posted earlier, just to see if anyone could notice a mistake.
Similar methods have been used in literature earlier, except that a
DFT calculation was made for the mono-anionic phosphate group to get
new charges. The DFT did reveal that charges on DOPA were similar to
DOPC.
The main issue I have is that I get a somewhat skewed phosphate
group that leads to unfavorable positions for the oxygen atoms on
phosphate. I am guessing that this is because of the bonded-
interactions of the new H-atom.
On Mon, May 5, 2008 at 3:10 PM, Mark Abraham
<[EMAIL PROTECTED]> wrote:
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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Maria G.
Technical University of Denmark
Copenhagen _______________________________________________
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