On 9/27/12 7:07 PM, pauladelgado wrote:
*file alfadrest.itp*
[ distance_restraints ]
; i j ? label funct lo up1 up2 weight
8002 10641 1 0 1 0.4 0.5 0.6 1
8040 10616 1 0 1 0.4 0.5 0.6 1
8067 10582 1 0 1 0.4 0.5 0.6 1
8104 10554 1 0 1 0.4 0.5 0.6 1
8283 10698 1 0 1 0.4 0.5 0.6 1
8259 10723 1 0 1 0.4 0.5 0.6 1
8222 10764 1 0 1 0.4 0.5 0.6 1
8189 10794 1 0 1 0.4 0.5 0.6 1
*file topol.top*
; Include Distance restraint file
#ifdef DISRES
#include "alfadrest.itp"
#endif
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "gromos43a1.ff/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 topology for ions
#include "gromos43a1.ff/ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein_chain_A 1
All of this appears normal. What about the question I posed before regarding an
energy contribution from the restraints? Do you see it in the .log or .edr
files? What is its magnitude?
*file .mdp*
; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run
define = -DDISRES
; 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
emstep = 0.01 ; Energy step size
nsteps = 500000 ; Maximum number of (minimization)
steps to perform
energygrps = Protein ; 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 and
long range
forces
ns_type = grid ; Method to determine neighbor list (simple,
grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range
forces)
coulombtype = PME ; Treatment of long range electrostatic
interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
;Parametros distance restraint
disre = simple ; simple (per-molecule) distance restraints
disre_fc = 1000 ; Force constant for distance restraints
*Questions*
1.When I am doing the minimization it comes out this 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.
Steepest Descents converged to machine precision in 349 steps,
but did not reach the requested Fmax < 10.
/
What this implies, can i continue besides this message?Or it is better to do
something about it?
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
2.Can you recomend considerable literature on vacuum simulation?
A simple Google search turns up lots.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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