[gmx-users] Adjust time intervals

[afsaneh maleki]

Thanks Dear Peter and Justin for reply,
I paste some text from .mdp for calculation of free energy. I have
done calculation of minimization energy before.


title	                	=      production for ile-pro-SOL
; Run parameters
integrator	          = sd		; leap-frog integrator
nsteps		          = 1000000	; 0.002* 1000000 = 2000 ps (2 ns)
dt		                = 0.002		; 2 fs
tinit                   =0
; Output control
nstxout		            = 100000		; save coordinates every 0.2 ps
nstvout                 =100000		; save velocities every 0.2 ps
nstxtcout               =100000		; xtc compressed trajectory output every 2 ps
nstenergy	        = 10000		; save energies every 0.2 ps
nstlog		        = 10000		; update log file every 0.2 ps
xtc_precision       =1000
; Bond parameters
constraint_algorithm   = lincs	; holonomic constraints
constraints	           = all-bonds	; all bonds (even heavy atom-H
bonds) constrained
lincs_iter	= 2          	; accuracy of LINCS
unconstrained_start        =no
lincs_order                =12
lincs_warnangle            =30
shake-tol                   =0.0001
; Neighborsearching
ns_type		          = grid	; search neighboring grid cels
nstlist		          = 10		; 10 fs
rlist		          = 1.2		; short-range neighborlist cutoff (in nm)
rcoulomb	          = 1.2		; short-range electrostatic cutoff (in nm)
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r                = 1.2
; Method for doing Van der Waals =
vdw-type                 = switch
; cut-off lengths        =
rvdw-switch              = 1.
rvdw                     =1.1
; Electrostatics
coulombtype	          = PME		; Particle Mesh Ewald for long-range electrostatics
; EWALD/PME/PPPM parameters =
pme_order                = 6
ewald_rtol               = 1e-06
epsilon_surface          = 0
optimize_fft             = no
fourierspacing	        = 0.16		; grid spacing for FFT
; Temperature coupling is on
;tcoupl		          = Nose-Hoover		; More accurate thermostat
;pcoupl	              =Parrinello-Rahman     ; Pressure coupling on in NPT
pcoupltype	         = isotropic
tau_p		         = 5.0			; time constant, in ps
ref_p		         = 1.0	   		; reference pressure, x-y, z (in bar)
compressibility          = 4.5e-5	  	; isothermal compressibility, bar^-1
;restraints
;dihre=simple
dihre-fc=1
nstdihreout=1000
disre=simple
disre_fc=1
; Periodic boundary conditions
pbc	                  = xyz		; 3-D PBC
; Dispersion correction
DispCorr	           = EnerPres	; account for cut-off vdW scheme

Thanks,
Afsaneh

On 3/25/12, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Peter C. Lai wrote:
>> In the .mdp file what is nstenergy set to?
>>
>
> I'd further ask what the rest of the .mdp file says, as well.  If this is
> the
> output of energy minimization, it's totally normal.  The output seems
> irregular
> but is due (I believe) to the potentially uneven step size taken during EM.
>
> -Justin
>
>> On 2012-03-25 04:37:59PM +0430, afsaneh maleki wrote:
>>> Dear users,
>>>
>>>
>>> When I got "total energy.xvg" file for plotting total energy via time,
>>> data haven't saved in order time intervals. What command can control
>>> time intervals in .mdp for .edr file? To better understand I pasted
>>> some text from "total energy.xvg" file. As you see, time intervals
>>> aren't same.
>>>
>>> @ s0 legend "Total Energy"
>>>     0.000000  -274454.750000
>>>    12.420001  -274884.187500
>>>    18.060001  -274532.343750
>>>    20.000000  -274475.437500
>>>    29.360001  -275739.562500
>>>    35.000000  -274441.937500
>>>    40.000000  -274463.156250
>>>    46.280003  -273342.250000
>>>    51.920002  -273099.718750
>>>    57.580002  -274429.250000
>>>    60.000004  -274844.062500
>>>    68.860001  -273905.093750
>>>    74.500000  -273988.812500
>>>    80.000000  -276057.625000
>>>
>>> Thanks very much in advance
>>> Afsaneh
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>
> --
> ========================================
>
> 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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