[gmx-users] Re: Difficulty running test particle insertion calculation

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 6 22:33:51 CEST 2009

The integrator in your .mdp file is "md" when it should be "tpi."


Jack Roberts wrote:
> I have now also tried defining separate energygrps in the input file 
> thinking this was possibly a energy/charge group related issue, but I am 
> still having no success.  I still receive the same error.
> Any constructive responses would be helpful at this point.
> On Thu, Aug 6, 2009 at 12:04 PM, aeBie8zo aeBie8zo <aebie8zo at gmail.com 
> <mailto:aebie8zo at gmail.com>> wrote:
>     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 (1537)
>     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,
>     Jack
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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