Nancy wrote:
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?


Try "constraints = all-bonds."  You should not use -DFLEXIBLE when running 
dynamics.

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?


Thermostats require sufficient degrees of freedom to sample a correct distribution. Coupling one molecule to a thermostat is incorrect. In this case, "tc-grps = System" is probably reasonable.

-Justin


Nancy



On Sat, Aug 8, 2009 at 3:49 PM, Justin A. Lemkul <jalem...@vt.edu <mailto: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 <http://vt.edu> | (540) 231-9080
    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

    ========================================
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--
========================================

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

========================================
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