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
--- Begin Message ---
Hello everyone,
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.
Prema.
--- End Message ---
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