[gmx-users] Energy minimization Error

[francesca vitalini]

Hi all!
I'm trying to run some energy minimization with gromacs 3.3.1 on a system
that I have transformed from cg to aa. After the reverse transformation I
solvate the system and I try to minimize just the proteins (my system is a
dimer) keeping fixed the water. Then the idea would be to minimize the
water keeping the protein in harmonic distance constraints as I just want
to obtain an aa system which describes the configuration obtained
previously in the cg representation.
So, I first use genrestr to create the .itp file for fixing the position of
the water, then I run 10 ps of EM and what I get is the following error
message:

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

>From what I've read in previous posts the problem might be either in the
mdp file or in the topology, but I don't understand what have I made wrong.
Here is my mdp file

 Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment

title           = Energy Minimization   ; Title of run

; The following line tell the program the standard locations where to find
certain files
cpp             = /lib/cpp      ; Preprocessor

; Define can be used to control processes
define          = -DEPOSRES
;define           = -DFLEXIBLE
; Parameters describing what to do, when to stop and what to save
integrator      = steep         ; Algorithm (steep = steepest descent
minimization)
emtol           = 10.0          ; Stop minimization when the maximum force
< 1.0 kJ/mol
dt                       = 0.005
;nsteps                   = 2000
nsteps          = 5000          ; Maximum number of (minimization) steps to
perform
nstenergy       = 1             ; Write energies to disk every nstenergy
steps
energygrps      = System        ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist         = 1             ; Frequency to update the neighbor list
ns_type         = grid          ; Method to determine neighbor list
(simple, grid)
coulombtype     = Reaction-Field ; Treatment of long range electrostatic
interactions
epsilon_rf      = 78
rcoulomb        = 1.4           ; long range electrostatic cut-off
rvdw            = 1.4           ; long range Van der Waals cut-off
constraints     = none          ; Bond types to replace by constraints
pbc             = xyz           ; Periodic Boundary Conditions (yes/no)

table-extension = 1.2

and this is my topology

;
;       File 'dynamin_dimer_fg.top' was generated
;       By user: vitalini (213883)
;       On host: goat
;       At date: Mon Jan 30 11:02:21 2012
;
;       This is your topology file
;       "The Poodle Chews It" (F. Zappa)
;
; Include forcefield parameters
#include
"/home/cocktail/vitalini/gromacs_special/share/gromacs/top/ffG53a6m.itp"

; Include chain topologies
#include "dynamin_dimer_fg_A.itp"
#include "dynamin_dimer_fg_B.itp"

; Include water topology
#include "/home/cocktail/vitalini/gromacs_special/share/gromacs/top/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif


;Include restraints on water
#ifdef POSRES_WAT
#include "posre_wat.itp"
#endif

; Include generic topology for ions
#include
"/home/cocktail/vitalini/gromacs_special/share/gromacs/top/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
;SOL              390842
SOL             390820
NA+                22

while this is the posre_wat.itp file I generated with genrestr

; position restraints for non-Protein of Protein in water

[ position_restraints ]
;  i funct       fcx        fcy        fcz
15231    1       1000       1000       1000
15232    1       1000       1000       1000
15233    1       1000       1000       1000
15234    1       1000       1000       1000
15235    1       1000       1000       1000
15236    1       1000       1000       1000
15237    1       1000       1000       1000
15238    1       1000       1000       1000
15239    1       1000       1000       1000
15240    1       1000       1000       1000
15241    1       1000       1000       1000
15242    1       1000       1000       1000
15243    1       1000       1000       1000
15244    1       1000       1000       1000
15245    1       1000       1000       1000
15246    1       1000       1000       1000
15247    1       1000       1000       1000
15248    1       1000       1000       1000
15249    1       1000       1000       1000
15250    1       1000       1000       1000
15251    1       1000       1000       1000
..........................
187712    1       1000       1000       1000

Any help?
Thanks Francesca


-- 
Francesca Vitalini

PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin

vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de

+49 3083875776
+49 3083875412
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