[gmx-users] g_order for lipid bilayers

Felipe Pineda, PhD luis.pinedadecastro at lnu.se
Wed Feb 20 16:31:36 CET 2013

Hi again,

my topology is non-consecutively numbered. I was looking for a tool to 
renumber it, but didn't find it yet. A hint will be really appreciated. 
I was not sure either whether or not is it possible to use the xtc 
generated with the original topology with the renumbered one. My main 
doubt is how to properly generate the index file for g_order. If each 
group contain an atom type in the chain, let's say all C21, another all 
C22, etc., I get many warnings of the type:

WARNING: distance between atoms 6767 and 6751 > 0.3 nm (1.406577). Index 
file might be corrupt.

If all atoms belonging to one chain are put together in a group, then 
the xvg files are empty.

There should be some posting in the archive clarifying the issue, but 
was not able to find it yet.



On 02/20/2013 04:17 PM, Justin Lemkul wrote:
> On 2/20/13 9:41 AM, Felipe Pineda, PhD wrote:
>> Hi,
>> is it possible to apply g_order to a trajectory of a lipid bilayer when the
>> carbon atoms of the acyl chains of the lipid molecules for which the SCD should
>> be calculated are not numbered consecutively, i.e. the atom numbers
>> corresponding to C21-C22-C23-... (sn-2 chain) are eg  23   22 19 ...  and these
>> appear in the corresponding group of the index file?
> Theoretically the bonded structure should be taken from the .tpr file, but you
> should probably do a quick test to be sure (i.e. consecutively numbered topology
> vs. nonconsecutive).
> -Justin

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