While minimising ethylene glycol, I have no defines, and constraints are set to none. During equilibration, define is set to -DFLEXIBLE, and constraints are set to all-angles. Which parameters would affect hydrogen bonding?
I have one glycerol molecule in the center of a box of 609 water molecules; what type of thermostat is reasonable for such a system? Nancy On Sat, Aug 8, 2009 at 3:49 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Nancy wrote: > >> Hello, >> >> I have successfully minimised and equilibrated ethylene glycol in a water >> box. I have noticed that there seem to be no hydrogen bonds between the >> solute and solvent, but there are hydrogen bonds forming and breaking >> between solvent molecules. Is this a normal behavior during minimsation and >> equilibration? >> >> > That will depend on whether or not you are position-restraining your > ethylene glycol, and whether or not your parameters are consistent with the > derivation of the force field. > > <snip> > > Steepest Descents converged to machine precision in 7007 steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = -3.3459230e+04 >> Maximum force = 4.9560604e+01 on atom 4 >> Norm of force = 3.4399371e+00 >> =============================================================== >> >> As I believe these forces to be acceptable, I proceed to equilibration: >> >> > These values appear to be reasonable, yes. > > $ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr >> >> where my "nvt.mdp" file is: >> > > rvdw = 1.3 >> > > As I've said before, this value of rvdw is not what is expected when using > the G53a6 parameter set. Unless you've got a good reason for altering the > original force field specifications, generally this is not a good idea. > > tcoupl = V-rescale >> tc-grps = GOL SOL >> > > How many glycerol molecules do you have? If it is only a small fraction of > the system, this treatment of thermostats is likely not appropriate. See > here: > > http://oldwiki.gromacs.org/index.php/thermostats > > <snip> > > =============================================================== >> Step 0, time 0 (ps) LINCS WARNING >> > > The procedure for solving a LINCS warning is always the same. Identify > where things start to fall apart, then verify that your topology is correct, > and your .mdp parameters are reasonable. I've made a few comments on .mdp > parameters above. As for the topology, that still remains a mystery. > Having never used topolbuild, I don't know how it assigns parameters, so it > may work just fine. But in general, this is always part of the diagnosis. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > 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/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/mailing_lists/users.php >
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