[gmx-users] dynamic selection memory allocation problem

Teemu Murtola teemu.murtola at gmail.com
Tue Jul 1 06:26:13 CEST 2014

Please try 'gmx gangle'. It does not have all the functionality of 'gmx
angle', which is why the old tool has not been replaced completely.

On Mon, Jun 30, 2014 at 11:03 PM, gigo <gigo at ibb.waw.pl> wrote:

> Dear Teemu,
> Thank you very much for the reply and such a fast patching of the sources.
> I have another question. Are there any plans for importing the dynamic
> selection scheme into the "angle" command?
> Best,
> g
> On 2014-06-29 06:58, Teemu Murtola wrote:
>> There were some hardcoded string buffers left from C days that were
>> necessary for error handling that placed a somewhat arbitrary limitation
>> of
>> 1024 characters per a single selection.
>> For the matter of what you are trying to achieve, you can probably do that
>> with gmx distance (with or without the fix for the limitation from
>> Gerrit),
>> but that tool may not be that well suited for the task. On purpose, I did
>> not add functionality to do 1-to-many or many-to-many distances there,
>> since that would better fit into another tool (which I or anyone else has
>> not had time to write yet), but it seems that this is the functionality
>> you
>> desire.
>> I would probably write a custom tool (based on the installed
>> share/gromacs/template) that would actually calculate the properties you
>> want, based on a selection that provides the ligand atoms of interest and
>> the water molecules you want, but I understand that not everyone is fluent
>> in C/C++.
>> If your system is big, you can probably also make your selection
>> substantially more effective by using multiple selections (it does not
>> appear that you actually need the plus keyword if you are only interested
>> in the -oall output) and a variable for the part after "or" that is always
>> evaluated for ~all atoms:
>>   ligand_p = resname LIG and name P;
>>   resid 14497 and resname SOL and name LP1 or ligand_p;
>>   resid 14497 and resname SOL and name LP1 or ligand_p;
>>   resid 14497 and resname SOL and name LP1 or ligand_p;
>>   ...
>> It also sounds that your script probably already has knowledge of the atom
>> indices, so it could generate the selection to use those directly.
>>  --
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