[gmx-users] Re: "Fmax (Andrea Bacconi)"

4tejender 4tejender at indiatimes.com
Sun Jan 23 17:50:33 CET 2005

hello Andrea
  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 
#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

insead of 
#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
Andrea Bacconi

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