[gmx-users] Re: distance restraint

[Justin Lemkul]

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

-- 
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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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