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