[gmx-users] spatial distribution function

prema.a at iiserpune.ac.in prema.a at iiserpune.ac.in
Tue Mar 6 07:03:18 CET 2012

                    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.

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