[gmx-users] Temperature Annealing
abdus sabuj
sabujbuetche at gmail.com
Mon Jan 25 22:33:33 CET 2016
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
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
>>>>>>
>>>>>> * Please search the archive at
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>>>>>> posting!
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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
>>>
>>> ==================================================
>>>
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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
>
> * Please search the archive at
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