[gmx-users] Conflicting atom names when using g_density

Bin Liu fdusuperstring at gmail.com
Wed Oct 23 03:05:21 CEST 2013

Hi Everyone,

I am having an awkward situation. I want to use g_density to get the
density profile of a lipid bilayer. At first glance, it looks like a
trivial task. But for my case, it's not because I have conflicting atom
names from two different molecules. I am using GROMOS 53a6. In DPPC
topology, I have C1 C2 C3 N4...O7...
In another lipid topology, say lipid B, I have C1 C2 C3 N4... C7...

The C1 in DPPC and C1 in lipid B could have different atomic mass as GROMOS
is united atom representation. C1 of DPPC could be a CH2, C2 of lipid B
could be a CH3. Then I don't know how to specify the entry in the .dat file:

C1 = ?

Is it possible to calculate the density profile of the whole bilayer by
just invoking g_density once? Or in my awkward situation, I have to
calculate the density profile of each molecule type, then add them
together? Then I will be concerned with the numerical errors involved.



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