[gmx-users] Adjust time intervals
Justin A. Lemkul
jalemkul at vt.edu
Sun Mar 25 16:08:00 CEST 2012
afsaneh maleki wrote:
> Dear Justin,
>
> I use version 4.0.7
>
I don't recall any specific bug related to this problem, but when using outdated
software (several years old in this case), the first step is to upgrade to the
newest version and try again. Development in the 4.0.x series is no longer
ongoing, so fixing any potential bugs there is not likely to happen. If the
problem is reproducible in the newest version, it will need to be investigated
further.
-Justin
> 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
>>
>> ========================================
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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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