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 <[email protected]> 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 >> >> > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
