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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