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

[Rasmus "Termo" Lundsgaard]

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
>
>