[gmx-users] Conflicting atom names when using g_density

Justin Lemkul jalemkul at vt.edu
Wed Oct 23 03:19:28 CEST 2013

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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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