[gmx-users] Adjust time intervals

[Justin A. Lemkul]

afsaneh maleki wrote:
> 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.
> 

Which Gromacs version are you using?  I can't reproduce your problem with 
version 4.5.4 or 4.5.5, either with or without the free energy code.  My energy 
outputs are always present at the nstenergy interval.

-Justin

> 
> 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
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> --
>> ========================================
>>
>> 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
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
> 

-- 
========================================

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

========================================