[gmx-users] SImulation error grompp

sunny mishra mishra.sunny at gmail.com
Thu Jan 14 19:17:57 CET 2010

I have updated the .top file as well after removing all the overlapping
lipids from .gro file

On Thu, Jan 14, 2010 at 10:15 AM, <chris.neale at utoronto.ca> wrote:

> Probably you removed lipids from the gro but not from the top (which you
> need to do as well).
> Find a lipid atom name that occurs only once per molecule (In non-united
> atom lipids I use P8)
> grep P8 my.gro |wc -l
> This will tell you how many lipids should appear in your top file.
> Chris.
> -- original message --
> 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)
> and it keeps on going until 2116 atoms.
> I dnt know how to fix this. Reply will be appreciable.
> Thanks,
> Sunny
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