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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