[gmx-users] Temperature Annealing
Justin Lemkul
jalemkul at vt.edu
Mon Jan 25 22:42:59 CET 2016
On 1/25/16 4:33 PM, abdus sabuj wrote:
> Hi Justin,
>
> I have used these following commands in npt and final .tpr production.
>
> grompp -f npt.mdp -p topol.top -c nvt.gro -o npt.tpr
>
>
> grompp -f final.mdp -p topol.top -c npt.gro -o final.tpr
>
...which explains everything. You're not preserving the state of the previous
equilibration (NPT). So your initial condition is nonsense, coupled with the
fact that Nose-Hoover allows for large fluctuations, suggests that your "final"
run is simply not reasonable. Pass the npt.cpt to grompp -t when generating the
annealing input. The fact that the initial temperature was not what you
expected should have been a red flag that something was wrong.
-Justin
> Thanks,
> Sabuj
>
>
> On Mon, Jan 25, 2016 at 1:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/25/16 2:41 PM, abdus sabuj wrote:
>>
>>> Hi Justin,
>>>
>>> Here is the mdp file I used for NPT equilibration...
>>>
>>>
>>> integrator = md
>>> nsteps = 10000000
>>> dt = 0.001
>>> nstenergy = 1000
>>> nstxout = 1000
>>> nstvout = 1000
>>>
>>>
>>>
>>>
>>>
>>> vdw-type = cut-off
>>>
>>>
>>> continuation = yes ; first dynamics run
>>> constraint_algorithm = lincs ; holonomic constraints
>>> constraints = all-bonds ; all bonds (even heavy atom-H
>>> bonds) constrained
>>> ;lincs_iter = 1 ; accuracy of LINCS
>>> ;lincs_order = 4 ; also related to accuracy
>>> lincs-warnangle = 90 ; warning after rotating the bond
>>>
>>>
>>> ns_type = grid ; search neighboring grid cels
>>> nstlist = 10 ; 10 fs
>>> rlist = 1.4 ; short-range neighborlist cutoff (in nm)
>>> rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
>>> rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
>>> coulombtype = PME ; Particle Mesh Ewald for long-range
>>> electrostatics
>>> pme_order = 4 ; cubic interpolation
>>> fourierspacing = 0.16 ; grid spacing for FFT
>>>
>>> ; set temperature to 300K
>>> tcoupl = v-rescale
>>> tc-grps = system
>>> tau-t = 0.1
>>> ref-t = 300
>>> ; and pressure to 1 bar
>>> pcoupl = berendsen
>>> ref-p = 1
>>> compressibility = 4.5e-5
>>> tau-p = 5
>>> ; generate initial velocities
>>> gen-vel = no
>>> ;gen-temp = 300
>>> ;gen_seed = -1
>>> ; Periodic boundary conditions
>>> pbc = xyz ; 3-D PBC
>>> ; Dispersion correction
>>> DispCorr = EnerPres ; account for cut-off vdW scheme
>>>
>>> ; COM motion removal
>>> ; These options remove motion of the protein/bilayer relative to the
>>> solvent/ions
>>> nstcomm = 1
>>> comm-mode = Linear
>>> comm-grps = system
>>>
>>>
>>> ...................................................................................................
>>>
>>>
>>> And for Production run, I am using the mdp file as below....
>>>
>>>
>>> integrator = md
>>> nsteps =10000000
>>> dt = 0.001
>>> nstenergy = 1000
>>> nstxout = 1000
>>> nstvout = 1000
>>>
>>>
>>> vdw-type = cut-off
>>>
>>> continuation = yes ; first dynamics run
>>> constraint_algorithm = lincs ; holonomic constraints
>>> constraints = all-bonds ; all bonds (even heavy atom-H
>>> bonds) constrained
>>> ;lincs_iter = 1 ; accuracy of LINCS
>>> ;lincs_order = 8 ; also related to accuracy
>>> lincs-warnangle = 90 ; warning after rotating the bond
>>>
>>>
>>> ns_type = grid ; search neighboring grid cels
>>> nstlist = 10 ; 10 fs
>>> rlist = 1.4 ; short-range neighborlist cutoff (in nm)
>>> rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
>>> rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
>>>
>>> coulombtype =PME ; Particle Mesh Ewald for long-range
>>> electrostatics
>>> pme_order = 4 ; cubic interpolation
>>> fourierspacing = 0.16 ; grid spacing for FFT
>>>
>>> ; set temperature to 300K
>>> tcoupl = Nose-Hoover
>>> tc-grps = system
>>> tau-t = 0.2
>>> ref-t = 300
>>> ; and pressure to 1 bar
>>> pcoupl = Parrinello-Rahman
>>> ref-p = 1
>>> compressibility = 4.5e-5
>>> tau-p = 5
>>> pcoupltype = isotropic
>>> ; generate initial velocities
>>> gen-vel = no
>>> ;gen-temp = 300
>>> ;gen_seed = -1
>>> ; Periodic boundary conditions
>>> pbc = xyz ; 3-D PBC
>>> ; Dispersion correction
>>> DispCorr = EnerPres ; account for cut-off vdW scheme
>>>
>>> ;simulated anneling
>>> annealing = single
>>> annealing-npoints = 6
>>> annealing-time = 0 2000 4000 6000 8000 10000
>>> annealing-temp = 300 310 320 330 340 350
>>>
>>> ; COM motion removal
>>> ; These options remove motion of the protein/bilayer relative to the
>>> solvent/ions
>>> nstcomm = 1
>>> comm-mode = linear
>>> comm-grps = system
>>> cos-acceleration = 0.01
>>>
>>>
>>> ...............................................................
>>>
>>>
>> And does your grompp invocation correctly pass the equilibration
>> checkpoint when preparing the production .tpr file? This is why I asked
>> for commands, too.
>>
>>
>> -Justin
>>
>> Thanks,
>>> Sabuj
>>>
>>>
>>> On Mon, Jan 25, 2016 at 12:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 1/25/16 1:51 PM, abdus sabuj wrote:
>>>>
>>>> Hi Mark,
>>>>> I have equilibrated my system very well before the production run at
>>>>> 300K,
>>>>> but at time zero, the temperature is at 321K.
>>>>>
>>>>> Here is the fluctuations I am getting.
>>>>>
>>>>> time (ns) temperature (K)
>>>>> 0 321
>>>>> 2 315
>>>>> 4 333
>>>>> 6 358
>>>>> 8 377
>>>>> 10 397
>>>>>
>>>>>
>>>>> Please provide the full .mdp file, rather than just the few lines you
>>>> think are important, as well as the commands used to continue from the
>>>> previous run. You probably have other incorrect settings and/or are
>>>> continuing the run wrong. Time zero should match the previous state; the
>>>> fact that it doesn't suggests you're not doing what you think you're
>>>> doing.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> Thanks,
>>>>
>>>>> Sabuj
>>>>>
>>>>> On Mon, Jan 25, 2016 at 12:38 PM, Mark Abraham <
>>>>> mark.j.abraham at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>>>
>>>>>> What fluctuations were you seeing over the time segments?
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>> On Mon, 25 Jan 2016 19:25 abdus sabuj <sabujbuetche at gmail.com> wrote:
>>>>>>
>>>>>> Dear gmx users,
>>>>>>
>>>>>>>
>>>>>>> I am trying to get viscosity as a function of temperature. So I have
>>>>>>> put
>>>>>>> the following annealing inputs to the mdp file.
>>>>>>>
>>>>>>> ;simulated anneling
>>>>>>> annealing = single
>>>>>>> annealing-npoints = 6
>>>>>>> annealing-time = 0 2000 4000 6000 8000 10000
>>>>>>> annealing-temp = 300 310 320 330 340 350
>>>>>>>
>>>>>>> i.e, at 10ns, the temperature should be at 350K, right? But I saw
>>>>>>> after
>>>>>>>
>>>>>>> my
>>>>>>
>>>>>> npt simulation that, the last temperature reached at 400K. Why that's
>>>>>>> happening, did I make any mistakes?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Sabuj
>>>>>>> --
>>>>>>> Gromacs Users mailing list
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>>>>>>>
>>>>>> Gromacs Users mailing list
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>>>>>>
>>>>>>
>>>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 629
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
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>>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
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>>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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