[gmx-users] Problem with g_density

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Apr 8 21:11:58 CEST 2010

1. Please include the actual commands that you used via copy and paste  
so that we can see *exactly* what you did.

2. Please include a snippit of the *actual* output identifying where  
the difference is that you mention here.

3. Note that g_density has some limitations, all related to volume  
3a. It doesn't account for volume fluctuations when normalizing the  
counts to get the density (not a problem for NVT):

   for (n =0; n < nr_grps; n++) {
     for (i = 0; i < *nslices; i++)
       (*slDensity)[n][i] = (*slDensity)[n][i] * (*nslices) /
         ( nr_frames * box[axis][axis] * box[ax1][ax1] * box[ax2][ax2]);

3b. Even if you center your bilayer along Z (with this program or with  
trjconv preprocessing), the bilayer center may fluctuate along z  
because bin numbering always starts at the bottom of the box (not a  
problem for NVT):

         /* determine which slice atom is in */
         slice = (int)(z / (*slWidth));
         (*slDensity)[n][slice] += top->atoms.atom[index[n][i]].m;



--original message --

Dear gmx-users,

I have generated 40ns trajectories for DPPC bilayer - water system. The
whole 40ns was generated in small trajectories and finally I concatenated
all the small trajectories to a big 40 ns trajectory using the following
options in trjcat

trjcat   -f   -o   -settime   -tu

Now the problem is when I am trying to plot partial density along the
bilayer - water interface axis (i.e. Z) using the big trajectory  for
different groups (e.g., water,DPPC etc.), density for water comes around 150
kg/m^3. But for any of the small trajectories the value is ok (i.e. around
1000). The plots were done using the folloing tool

    g_density   -f    -o   -n   -s  -d Z

Can anyone help?

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