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 <jalem...@vt.edu <mailto:jalem...@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.abra...@anu.edu.au
        <mailto:mark.abra...@anu.edu.au>
        <mailto:mark.abra...@anu.edu.__au
        <mailto:mark.abra...@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







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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 <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>

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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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