HI Chris I followed the steps below and when i tried to run g_spatial it executed g_cluster instead. Even when i do g_spatial -h it looks like its being overwritten by g_cluster
1.I used make_ndx to create a group containing the atoms around which i want the SDF 2. trjconv -s md.tpr -f tyrc_md.trr -o tyrc1.xtc -center tric -ur compact -pbc none 3. trjconv -s md.tpr -f tyrc1.xtc -o tyrc2.xtc -fit rot+trans 4. g_spatial -s md.tpr -f tyrc2.xtc -n index.ndx I wrote g_spatial and it should produce a spatial distribution function. However, it's rather complicated to use. Did you follow the directions in g_spatial -h ? There are about 10 steps to use it. It is so complicated on purpose in order to give the user full flexibility, but this means that you need to do all of your alignment yourself. If you did that correctly, then I also suggest that you should make sure that you are visualizing it correctly in VMD. By default you will see some atoms, but that is only there because VMD will not recognize a gaussian cube without any atoms, and also it makes it easier for you to ensure that any other pdbs you may load overlay correctly. Therefore ensure that you switch the representation to isosurface and then slide the bar so that you see the appropriate isosurface contour. Please report back to the list with findings so that other users can later benifit from your work Chris. Gadzikano Munyuki wrote: > I want to analyse the solvent around a peptide . I used g_sdf and > the output that i am getting (i.e the refmol.gro) does not have the > whole peptide molecule but just the residues that i use to define > the coordinate system . I then tried to use g_spatialbut its doing > something very different and not spatial distibution, it looks like > its executing g_cluster instead. I was wondering if g_custer and > g_spatial are meant to do the same thing. Have a read of g_cluster -h and g_spatial -h and decide whether they're doing the same thing :-) Mark ______________________________________________________________________________________________ UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 4500. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. _____________________________________________________________________________________________________ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
