[gmx-users] Difficulty running test particle insertion calculation

aeBie8zo aeBie8zo aebie8zo at gmail.com
Thu Aug 6 19:04:15 CEST 2009

I am attempting to run a test particle insertion calculation of Argon in
SPC/E water using GROMACS 4.0.3.  Here is what I have done so far:

   1. Generated a .trr file with a simulation of 512 SPC/E water molecules
   2. Added an Argon atom to the SPC/E .gro and .top files
   3. Used grompp to generate the .tpr file from the edited .gro and .top
   files in 2. above.
   4. Ran mdrun with the .tpr file from 3. and the options "-tpi" and
   passing the .trr file with "-rerun".

If I am understanding the manual correctly, this is all that needs to be
done.  However, on the last step I keep getting the error:

   - Number of atoms in trajectory (1536) does not match the run input file

I believe I am either making a simple error in the steps above or I'm
misunderstanding the manual.  The specific commands and relevant files are
all contained here:  http://wel-dhcp-145-159.cm.utexas.edu:8080/gmx-tpi.

If anyone could point out my error, I would greatly appreciate it.

Thank you,

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