[gmx-users] trjconv

[David]

On Wed, 2005-04-13 at 18:04 -0500, Dinesh Pinisetty wrote:
> 
> 
> 
> Hello Everybody,
>       I have simulated a DPPC bilayer system with water and a chemical for
> 50ns.When I used trjconv -f .xtc -s .tpr -center it asked me to select a
> group twice.(I want to center all the atoms of the chemical to plot its
> mass density profile).So I selected the chemical residue name both the
> times.It gave me a output file trajout.xtc.Now when I am using this output
> file to plot mass density profile of the chemical I get the following.
> 
> Reading frame    6110 time 12220.001   There were 1880 inconsistent shifts.
> Check your topology
> There were 1740 inconsistent shifts. Check your topology
> There were 1906 inconsistent shifts. Check your topology
> There were 1816 inconsistent shifts. Check your topology
> There were 1928 inconsistent shifts. Check your topology
> There were 1808 inconsistent shifts. Check your topology
> There were 1838 inconsistent shifts. Check your topology
> There were 1834 inconsistent shifts. Check your topology
> There were 1880 inconsistent shifts. Check your topology
>   Could anyone tell me where exactly the mistake might be in topology file
> because of which i am getting these inconsistent shifts.
Problem is in the xtc file. Since you centered all atoms molecules may
have been broken. A way around this could be making a tpr file with
pbc=full for the analysis, or, when using g_density, using the original
xtc file.

>   Any help would be greatly appreciated.
> Thanking you,
> Dinesh.
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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