[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.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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