[gmx-users] berendsen P coupling and fluctuation properties
katesedate at gmail.com
Wed Aug 17 05:27:19 CEST 2011
Thanks Justin for your thorough description. Is there any specific tool in
gromacs to plot histograms or you mean I follow the customary plotting
I have one more question. I am now trying using PR pressure scheme with
v-rescale thermostat for NPT dynamics. Before dynamics run, can I apply
berendsen barostat combined with v-rescale thermostat to equilibrate or
since I am using berendsen barostat, T coupling scheme has to be also
On 16 August 2011 13:17, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Elisabeth wrote:f
>> Thank you. I am looking at potential energies to calculate vaporization
>> heat. I wanted to know how the fact that berendsen does not lead to correct
>> ensemble is affecting total potential energy of the system. I have an
>> unclear image of "correct ensemble". Does this mean whatever output I am
>> getting from my runs are unreliable?
> The Berendsen coupling algorithms produce very narrow distributions of
> temperature and pressure. These do not correspond to the correct
> distribution of a true statistical mechanical ensemble; plot a histogram and
> you'll find that the results are shockingly different between Berendsen and,
> say, Nose-Hoover for T. Therefore, the ensemble you're using to measure
> your properties is not NPT (or NVT, in the case of thermostat only), it's
> something undefined and likely not real. Applying better thermostats and
> barostats that have been shown to produce the correct distributions is more
> rigorously correct.
> The effects are usually not terribly noticeable unless you go looking for
> them. You'll find that the Berendsen algorithms quite faithfully give you
> the target T and P that you desire (which does make them very good for
> initial equilibration) and so you naturally assume that everything is fine.
> While that's all well and good in one sense, the fluctuations of T (and
> thus velocities, and thus kinetic energy) are wrong. If KE does not
> fluctuate properly, then neither does PE (since you're then affecting energy
> flow between PE and KE, while total energy stays fixed, in theory).
> The larger point is that if you claim to apply an NVT (or NPT) ensemble
> using Berendsen coupling, you're not correct, strictly speaking.
> Appreciate any clarification.
>> Thank you,
>> On 15 August 2011 19:34, Mark Abraham <Mark.Abraham at anu.edu.au <mailto:
>> Mark.Abraham at anu.edu.**au <Mark.Abraham at anu.edu.au>>> wrote:
>> On 16/08/2011 7:05 AM, Elisabeth wrote:
>>> Dear all,
>>> I noticed that applying Parrinello-Rahman (PR) pressure coupling
>>> even after equilibration with berendsen does not lead to target
>>> value for pressure when
>>> ; Bonds
>>> constraints = none
>>> is used.
>> The use of constraints and the integration step size is linked.
>> Roughly speaking, no constraints should accompany a 0.5 fs time
>> step, H-bond constraints with 1fs and all constraints with 2fs.
>> Haphazard changes to .mdp files have all kinds of these "gotchas".
>> I tried Berendsen for to get fixed pressure ( 50 bar) but in the
>>> next run PR even for long time is giving 52 bar. This is the case
>>> for other target pressures too.
>> You need to be sure to collect statistics only after equilibration,
>> and consider whether the observed variation is consistent with
>> convergence to a given value.
>>> So this made me select Berenden which is giving target pressure
>>> values but my concern is whether my results are reliable because
>>> BR does not give the exact ensemble as PR. I read somewhere on the
>>> list that fluctuation properties can not be calculated when BR is
>>> used. What does "fluctuation property" mean?
>> BR does not produce the correct ensemble. I forget the details about
>> why, but there are references in the T-coupling section of the
>> manual you should consider.
>> Does this mean that any property calculated form fluctuations of
>>> some other quantity can not be obtained>? like heat capacity which
>>> is defined based on enthalpy fluctuations?
>> IIRC, yes.
>> I am interested in potential energy terms (g_energy bonded/non
>>> boned terms)
>> I routinely struggle to see why people think they can learn anything
>> from these.
>> and structural properties like rdf for a number of polymer
>>> molecules, system size around 3000 atoms.
>>> Thank you for your comments.
>>> constraints = none
>>> ; Run control integrator = md
>>> dt = 0.001 nsteps
>>> = 5000000 nstcomm = 100
>>> nstenergy = 100 nstxout =
>>> 100 nstlist = 10 ns_type
>>> = grid
>>> coulombtype = Shift vdw-type
>>> = Shift rcoulomb-switch = 0
>>> rvdw-switch = 0.9 ;0
>>> ; Cut-offs
>>> rlist = 1.25 rcoulomb =
>>> 1.0 rvdw = 1.0
>>> Tcoupl = v-rescale tc-grps
>>> = System tau_t = 0.1 ref_t
>>> = 300
>>> Pcoupl = berendsen Pcoupltype =
>>> isotropic tau_p = 1
>>> compressibility = 3.5e-5 ref_p = 10
>>> gen_vel = no
>>> gen_temp = 300.0 gen_seed =
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/**
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