[gmx-users] Adjust time intervals
afsaneh maleki
maleki.afsaneh at gmail.com
Sun Mar 25 15:32:19 CEST 2012
Dear Justin,
I use version 4.0.7
Thanks
Afsaneh
On 3/25/12, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
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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
>>>
>>> ========================================
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
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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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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