[gmx-users] Parrinello-Rahman and Simulated Annealing

[Baptiste Demoulin]

Thank your for your answer !

Actually yes, annealing is just a preparatory step, so I'll just keep
Berendsen barostat for the equilibration. I was just wondering about the
behaviour of Parrinello-Rahman. Thanks !

Baptiste


2013/5/21 Justin Lemkul <jalemkul at vt.edu>

>
>
> On 5/21/13 7:55 AM, Baptiste Demoulin wrote:
>
>> Dear Gromacs users,
>>
>> I am trying to simulate a large systems embeded in a membrane (roughly
>> 360,000 atoms). I would like to equilibrate it at 300K and 1 atm. To this
>> mean, I use simulated annealing to slowly warm up the system from 50 to
>> 300K, under NPT conditions.
>>
>> For the simulation, I use position restraints on the heavy atoms on the
>> protein, and stronger constraints on the metallic core, and LINCS to
>> constrain all the bonds, and 2 fs timestep.
>>
>> My problem is that when I use Parrinello-Rahman barostat for the
>> simulation, I got LINCS warning concerning the restrained metallic core.
>> However, using Berendsen barostat for the same system, same input, seems
>> to
>> work fine, (at least for the 200,900 steps I did until now). I thus tried
>> various modifications, such as changing the coupling tau_p, running first
>> a
>> pure NVT at 50K for 2 ps, and then warming, but that did not work... Is
>> there an incompatibility between Parrinello-Rahman and simulated annealing
>> ?
>>
>>
> Parrinello-Rahman allows for much wider fluctuations than the Berendsen
> algorithm, so I can see how warming the system may cause problems unless it
> is very well equilibrated beforehand.  Assuming that the annealing step is
> a preparatory step, there is no compelling need to use P-R, is there?  If
> there is, you may just have to do the annealing over a much longer time
> period such that the change in temperature is (very) long with respect to
> tau_p, to allow for the barostat to adjust to changing conditions.
>
> -Justin
>
>
>  Here is my input:
>>
>> define               = -DPOSRES -DPOSRES_CORE
>> integrator           = md
>> continuation         = no           ; first dynamics run
>> nsteps               = 1500000
>> dt                   = 0.002
>>
>> nstcomm              = 1
>> comm-mode            = linear
>> comm-grps            = Protein_POPC SOL_NA_CL
>>
>> pbc                  = xyz
>> nstlist              = 10
>> ns-type              = grid
>> rlist                = 1.0
>> rlistlong            = 1.6 ; the force on a particle which falls within
>> rlist and rlistlong is calculated during the pair list update and retained
>> during nslist steps
>> coulombtype          = pme
>> rcoulomb             = 1.0
>> vdwtype              = cut-off
>> rvdw                 = 1.4
>> DispCorr             = EnerPres
>>
>> nstxtcout            = 10
>> nstxout              = 0
>> nstvout              = 0
>> nstfout              = 0
>> nstlog               = 10
>>
>> constraints          = all-bonds
>> constraint-algorithm = lincs
>>
>> tcoupl               = V-rescale
>> tc-grps              = Protein POPC SOL_NA_CL
>> tau_t                = 0.1  0.1  0.1
>> ref_t                = 300  300  300
>>
>> pcoupl               = Parrinello-Rahman
>> pcoupltype           = semiisotropic
>> compressibility      = 4.5e-5 4.5e-5
>> tau_p                = 10.0
>> ref_p                = 1.0 1.0
>>
>> refcoord_scaling     = com
>>
>> gen_vel              = no
>> gen_temp             = 50
>> gen_seed             = -1
>>
>> annealing            = single single single
>> annealing_npoints    = 2 2 2
>> annealing_time       = 0 2000 0 2000 0 2000
>> annealing_temp       = 50 300 50 300 50 300
>>
>> Thank you very much for your help !
>>
>> Baptiste
>>
>>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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