[gmx-users] charge adjustment/ emtol /more groups /

Marco Landwehr tarowas at gmx.de
Tue Oct 26 19:14:14 CEST 2004

I am pretty new to  Gromacs. The tutorial is very nice, but trying out now
some real proteins leads towards questions. Trying to solve them with the
mail archive I am not very successful. So I post the question to the list.

trying to follow the tutorial steps on 2HPD (protein plus heme cofactor)
generates 3 problems/questions:

1) while turning the em.mdp (the one file I picked from the tutorial) file
into a run input file em.tpr
WARNING 1 [file "2HPD_A_minO.top", line 29198]:
  System has non-zero total charge: -1.500000e+01
-This seems to be a common problem. Do I have to add counter ions?
If yes, where to I have to add the counter NA ions (by hand?)?
Can I use genion on the em.tpr file to generate a new .gro file which is
then used for generating a new .top file?

2)While doing the Energy Minimization:
-->Converged to machine precision,
but not to the requested precision Fmax < 2000
-What is a reasonable Fmax/emtol value? Can I get to lower values just by
more steps?

3) During the MD-run:
Making dummy/rest group for T-Coupling containing 47 elements
Fatal error: Not enough ref_t and tau_t values!
- I know I have to generate another group. I probably have the protein, the
HEME and SOL. In the sample .mdp file for speptide there are only two
My topology file also lists only two groups:
; Name
?^M in water
; Compound  #mols
Protein_A   1
SOL    10487

But I dont know which name the additional groups have. How can I get these
names? The 47 elements origin from the HEME co-factor.

Thanks for your help


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