[gmx-users] Re: distance restraint

[pauladelgado]

*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
*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?

2.Can you recomend considerable literature on vacuum simulation?



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