[gmx-users] Re: Difficulty running test particle insertion calculation
aebie8zo at gmail.com
Thu Aug 6 22:25:47 CEST 2009
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>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,
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