[gmx-users] Temperature Annealing
abdus sabuj
sabujbuetche at gmail.com
Mon Jan 25 20:41:11 CET 2016
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
...............................................................
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
>>>> --
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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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