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
fluctuations:
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;
User-beware.
Chris.
--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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