On 10/22/13 9:05 PM, Bin Liu wrote:
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.
Assign unique names in the .top, create a new .tpr, and the problem is solved.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==
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