[gmx-users] Problem with g_chi options

Anna Stopka anna.stopka at student.kit.edu
Mon Jul 14 16:33:16 CEST 2014


Thanks for your reply Justin!
I have tried using a tpr file instead of a gro file, but that makes no 
difference. I still have the same problem!

Does anybody have another idea?
Thanks in advance!


On 07/09/2014 07:24 PM, Justin Lemkul wrote:
> On 7/9/14, 5:51 AM, Anna Stopka wrote:
>> Hi everybody,
>> I wrote last week, but nobody answered. So I write again, still having the same
>> problem:
>> I want do an analysis of my simulation with the tool g_chi.
>> The problem is, that the optional output options don't work.
>> I use the following command:
>> g_chi -s config.gro -f traj.xtc -oh -all
>> and all I get are the standard output files chi.log and order.xvg.
>> I am not sure if it has something to do with the following warning I get:
>> WARNING: not all dihedrals found in topology (only 1056 out of 1746)!
>> Honestly, I don't understand why I get this warning, because all the
>> input files are fine.
> Have you tried using a .tpr file instead of a .gro file as the structure passed
> to -s?  I don't know how there can be any interpretation of a topology, given
> the fact that you haven't passed any topological information to g_chi.
> -Justin

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