francesca vitalini wrote:
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
The other possibility is that there is no problem at all. Some systems cannot
be minimized below certain thresholds, based on the input geometry. You may
also want to try a different minimizer or double precision.
http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
-Justin
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
vital...@zedat.fu-berlin.de <mailto:vital...@zedat.fu-berlin.de>
francesca.vital...@fu-berlin.de <mailto:francesca.vital...@fu-berlin.de>
+49 3083875776
+49 3083875412
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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