[gmx-users] Series of questions
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
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
Hope some good soul out there can lend a hand.
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