[gmx-users] Series of questions

Raj Badhan r.k.badhan at stud.man.ac.uk
Tue Sep 16 19:18:00 CEST 2003

I have a few questions that I hope someone can answer.
OK, my system is setup in windows xp.
I'm running a simulation on a protein within a water box, using 
gromacs force fields.
I can get upto the point of where I have added the water and am 
beginning a position restrained MD simulation.I pre-processes the 
pr.mdp file (laid out as in the John Kerrigan tutorial except for an 
extra entry for a Cl counter ion).
At this point I get a number of errors:

system has non-zero total charge 1.80000000e+0.01.
I had to add a Cl counterion to balance up the +1 charge on the 
protein and dont understand why this error has occured.

and also, i get a error saying:

Fatal error:...no. of co-ordianted in co-ord. file doesnt match the 
topology file.

Now, I corrected the TOP file by removing one water and adding the 
entry for the Cl ion and adding ions.itp in the relevant place, and 
again, I dont understand why this error occurs.

When we add the counterion, according to the John Kerrigan 
tutorial, he has his output file from genion called fws_ion.gro.
Sould I be using this file (myprotein_ion.gro) to continue onto the 
energy minimisation and position-restrained sections?

I'd really appreciate any help as this is bugging the hell out of me!
I'd also like to be able to e-mail someone who could assit me 
through this stage of my simulations when required rather then 
sending endless e-mail to this message board and clogging up 
your servers.
Hope some good soul out there can lend a hand.
Many thanks!
Raj Badhan

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