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?
Appreciate any clarification. Thank you, Best, On 15 August 2011 19:34, Mark Abraham <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 > > > > > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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