[gmx-users] spatial distribution function

[prema.a at iiserpune.ac.in]

                    I am trying to calculate spatial distribution function (SDF) for ionic liquid.I want to see the distribution of anion around cation. I followed the steps given in gromacs manual.I created two groups each of single cation and all anions in the index file and did two steps trjconv_d to get trajectory for centered solute by removing translational and rotational degrees of freedom. When I am running g_spatial_d on this trajectory I am only able to see anions in my cube file as I am selecting anions for writing output co-ordinates. Am I following correctly or doing something wrong ? I am using updated gromacs version 4.5.4. Please I would really appreciate if someone can help this?
     Thank you in advance.
     Pre

-------------- next part --------------
An embedded message was scrubbed...
From: prema.a at iiserpune.ac.in
Subject: spatial distribution function
Date: Tue, 6 Mar 2012 11:09:56 +0530 (IST)
Size: 2843
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120306/12b752f7/attachment.mht>