[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
> 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:
> If anyone could point out my error, I would greatly appreciate it.
> Thank you,
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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