[gmx-users] SImulation error grompp

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 14 21:02:13 CET 2010

sunny mishra wrote:
> Hi All,
> I am running simulation of a system containing Coarse Grained 1SU4 
> (Minimized structure) and Coarse Grained DPPC lipid. I used the 
> INFLATEGRO script to inflate the lipid and removed the overlapping 
> lipids with proteins and then running the energy minimization.
> grommp says there are mismatching of atoms in system.top file (which 
> consists of DPPC, Protein and W) and inflated_bilayer.gro (Which 
> Inflategro script developed). I don't know why this is happening and why 
> the atoms are not matching. Also, is there any problem with the 
> atom2cg.awk script which MARTINI guys provided or they have any other 
> script which converts the atomic structure of protein to CG protein so 
> that at the time of simulation the atoms match.
> I am using the grompp command something like this.
> grompp -f em.mdp -c inflated_bilayer.gro -p system.top -maxwarn 10
> grompp says: atom name 1 in system.top and inflated_bilayer.gro does not 
> match (NC3-BCQd)

This is normal.  Please see the MARTINI documentation - it explicitly describes 
what each script, etc. is doing - the initial CG structure contains generic atom 
names, which are replaced in this step.

As a note, this is pretty much the *only* situation where mismatches are useful 
or appropriate.  Most of the time (as we have seen recently), mismatches lead to 
catastrophic problems later :)


> and it keeps on going until 2116 atoms.
> I dnt know how to fix this. Reply will be appreciable.
> Thanks,
> Sunny


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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