[gmx-users] g_sdf gives wrong refmol with multiple center molecules

[Ondrej Marsalek]

Hi,

just for reference, I have filed a bug report on this (and one other
issue with g_sdf):

http://bugzilla.gromacs.org/show_bug.cgi?id=356

Best,
Ondrej


On Tue, Nov 10, 2009 at 16:35, Rasmus "Termo" Lundsgaard
<termopeten at gmail.com> wrote:
> Hi Atte
>
> Did you find a solution to this problem?? I'm doing the same calculations as
> you describe, and wanted to try it out on TIP4p water first - which gives
> the wrong coordinates for the ref molecule by the -r flag as you
> described?!?
>
> The distribution looks completely right though...
>
> Anyone got an idea of where it goes wrong and how the .gro can be translated
> easily to the right center place??
>
> I have also tried using the g_spatial function. but here my problems stops
> on of how to make the xtc file with trjconv in a easy way so it will have
> each water molecule as the center molecule and a big xtc file. Right now I
> can do it for all time frames with one designated water molecule. this will
> only give me the distribution function around one water molecule - instead
> of using all of them... I would like all time frames for 1st water molecule,
> then all time frames for 2nd water molecules, etc. in one xtc file...
>
> Best regards
> Rasmus
>
>
>> Hi,
>>
>> if you give g_sdf just one molecule (in mode 1) to look at the
>> distribution of other atoms around it, everything looks fine. However, if
>> you give two or more molecules, the refmol.gro that is printed is messed up,
>> but the actual density map still looks ok. You can try this with the 216
>> water molecule tutorial case.
>>
>> Run a short md writing frames into traj.xtc.
>> Append these lines to the index.ndx (which has only OW group before
>> these).
>> [ O1 ]
>> 1  4
>> [ H1 ]
>> 2  5
>> [ H2 ]
>> 3  6
>>
>> or
>> [ O1 ]
>> 1
>> [ H1 ]
>> 2
>> [ H2 ]
>> 3
>>
>> give
>> g_sdf -s topol.tpr -f traj.xtc -n index.ndx -r
>> 2
>> 3
>> 4
>> 1
>> and have a look at the refmol.gro in the two cases.
>>
>> Is there something wrong in adding up the coordinates?
>>
>> Cheers,
>> Atte
>>
>>
>
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