[gmx-users] SImulation error grompp

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Jan 14 19:15:45 CET 2010

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.


-- 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.


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