[gmx-users] Re: "Fmax (Andrea Bacconi)"
4tejender at indiatimes.com
Sun Jan 23 17:50:33 CET 2005
i got your problem. when u r using congugatate gradient method you r not able to preprocess your solvated protein file that is due to because u haven't used flexible parameters for your solvent in the topology file.include these lines
#include "spc.itp" line in your topology file
and also don't forget to see wethere you have pointed
define = -DFLEX_SPC
in your mdp file or not
go ahead with it you will not get that error again
regarding your questions as per my knowlege
1.Fmax can be controlled by energy tolerence value in the mdp file.
2.regarding charge i must say u can balence it during pdb2gmx run by adding flags -lys, -his,-glu etc and manully choose particular residue to be as neutral or charged. but again it is diffult to assign charge which residue to choose for charged one. as i think outer residue should be given charge but that too should be conplementry to hydrogen bonding pattern otherwise u will get error thar no of donor and no of acceptor does not mathch with each other
3.i think third one is i had answered in first
Hallo to all the Gromacs users
I would like to ask some general questions about the meaning of the Fmax
value that you get after the energy minimization procedure. The
question is simple I want to simulate the beaviour of a protein (about
390 aa) in water solution; using the alghoritms like steepest descent
and l-bfgs I am not able to get an Fmax below 2000 no constraints were
settled (checked the tpr file and no CONS were found), instead I'm not
able to use cg at all because the program grompp complains about this
error: ERROR can not do conjugate gradients with constraints (29796).
I have such a kind of problem only when I introduce water because when I
am working with the protein alone I can go down with Fmax up to 50.
My questions are:
i) What is a reasonable value for Fmax to set for a MD simulation in
water? Is it there a general good Fmax rang of values or its changing
accordingly to the simulated system?
ii) When I convert the pdb file with pdb2gmx if I use option 0 I
always get extra charge to balance, which instead I don't get if I'm
using option 1 (G43b1 GROMOS96 43b1 Vacuum Forcefield). Is it ok to use
option 1 as forcefield, then solvate the previous output with water and
go for an energy minimization run?
iii) any suggestions on how to write a working em.mdp script with a
reasonable Fmax value?
I already posted some questions about this em problem and I got some
good suggestions but I was not able to solve it.
Thank you for your attention and great help
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