[gmx-users] berendsen P coupling and fluctuation properties
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 17 07:38:16 CEST 2011
Elisabeth wrote:
> Thanks Justin for your thorough description. Is there any specific tool
> in gromacs to plot histograms or you mean I follow the customary
> plotting procedure?
>
You have to write your own code from, e.g., g_energy output.
> 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
> berendsen?
>
You can use any combination you like during equilibration.
-Justin
> Thanks,
>
>
> On 16 August 2011 13:17, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Elisabeth wrote:f
>
> Hello,
>
> 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.
>
> -Justin
>
> Appreciate any clarification.
>
> Thank you,
> Best,
>
> On 15 August 2011 19:34, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.__au
> <mailto: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.
> Best,
>
> 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
> = 173529
>
>
>
>
>
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>
> http://lists.gromacs.org/__mailman/listinfo/gmx-users
> <http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at
> http://www.gromacs.org/__Support/Mailing_Lists/Search
> <http://www.gromacs.org/Support/Mailing_Lists/Search> before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at __gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
>
> Can't post? Read
> http://www.gromacs.org/__Support/Mailing_Lists
> <http://www.gromacs.org/Support/Mailing_Lists>
>
>
>
> --
> ==============================__==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================__==========
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/__mailman/listinfo/gmx-users
> <http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at
> http://www.gromacs.org/__Support/Mailing_Lists/Search
> <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
> <http://www.gromacs.org/Support/Mailing_Lists>
>
>
--
========================================
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list