francesca vitalini wrote:
Tryed the double precision without any success... Again the same type of
error message. Might need to try other minimization algorithm. Any
suggestions on that?
What is the Fmax you achieve, and what are your intents for this process?
Minimizing very low is only strictly necessary for certain types of very
sensitive calculations. For normal MD, convergence below 100-1000 kJ/mol-nm is
typical.
Other algorithms are listed in the manual. They may or may not be necessary.
-Justin
2012/2/9 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
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
<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>
<mailto:vital...@zedat.fu-__berlin.de
<mailto:vital...@zedat.fu-berlin.de>>
francesca.vitalini@fu-berlin.__de
<mailto:francesca.vital...@fu-berlin.de>
<mailto:francesca.vitalini@fu-__berlin.de
<mailto:francesca.vital...@fu-berlin.de>>
+49 3083875776 <tel:%2B49%203083875776>
+49 3083875412 <tel:%2B49%203083875412>
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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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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