Hello,<br><br>I have successfully minimised and equilibrated one glycerol molecule in a box of water (using the ".mdp" files below).<br><br>
I noticed that during both minimisation and equilibration, solvent
molecules (waters) form many more hydrogen bonds between each other
than the solute (glycerol) forms to the solvent molecules. Is this normal for
such a system?<br>
<br>
Thank you.<br>
<br>
Nancy<br><br><br>==========em.mdp==========<br>constraints = none<br>integrator = steep<br>nsteps = 10000<br><br>emtol = 10.0<br>emstep = 0.01<br> <br>nstlist = 2<br>
coulombtype = PME<br>nstcomm = 2<br><br>ns_type = grid<br>;rlist = 1.0<br>;rcoulomb = 1.0<br>;rvdw = 1.0<br>nstxout = 2<br><br>pbc = xyz<br>
pme_order = 4<br>==========em.mdp==========<br><br>==========nvt.mdp==========<br>title = Glycerol NVT equilibration <br><br>integrator = md<br>nsteps = 5000<br>dt = 0.002<br><br>nstxout = 10<br>
nstvout = 10<br>nstenergy = 10<br>nstlog = 10<br><br>continuation = no<br>constraint_algorithm = lincs<br>constraints = all-bonds<br>lincs_iter = 1<br>lincs_order = 4<br><br>ns_type = grid<br>
nstlist = 5<br><br>coulombtype = PME<br>pme_order = 4<br>fourierspacing = 0.16<br><br>tcoupl = V-rescale<br>tc-grps = System<br>tau_t = 0.1<br>ref_t = 300<br><br>pcoupl = no<br>
<br>pbc = xyz<br><br>DispCorr = EnerPres<br><br>gen_vel = yes<br>gen_temp = 300<br>gen_seed = -1<br>==========nvt.mdp==========<br><br><br><br><div class="gmail_quote">On Sat, Aug 8, 2009 at 4:49 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
Nancy wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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?<br>
<br>
</blockquote>
<br></div>
Try "constraints = all-bonds." You should not use -DFLEXIBLE when running dynamics.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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?<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Nancy<div><div></div><div class="h5"><br>
<br>
<br>
<br>
On Sat, Aug 8, 2009 at 3:49 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Nancy wrote:<br>
<br>
Hello,<br>
<br>
I have successfully minimised and equilibrated ethylene glycol<br>
in a water box. I have noticed that there seem to be no<br>
hydrogen bonds between the solute and solvent, but there are<br>
hydrogen bonds forming and breaking between solvent molecules.<br>
Is this a normal behavior during minimsation and equilibration?<br>
<br>
<br>
That will depend on whether or not you are position-restraining your<br>
ethylene glycol, and whether or not your parameters are consistent<br>
with the derivation of the force field.<br>
<br>
<snip><br>
<br>
<br>
Steepest Descents converged to machine precision in 7007 steps,<br>
but did not reach the requested Fmax < 10.<br>
Potential Energy = -3.3459230e+04<br>
Maximum force = 4.9560604e+01 on atom 4<br>
Norm of force = 3.4399371e+00<br>
===============================================================<br>
<br>
As I believe these forces to be acceptable, I proceed to<br>
equilibration:<br>
<br>
<br>
These values appear to be reasonable, yes.<br>
<br>
<br>
$ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr<br>
<br>
where my "nvt.mdp" file is:<br>
<br>
<br>
rvdw = 1.3<br>
<br>
<br>
As I've said before, this value of rvdw is not what is expected when<br>
using the G53a6 parameter set. Unless you've got a good reason for<br>
altering the original force field specifications, generally this is<br>
not a good idea.<br>
<br>
<br>
tcoupl = V-rescale<br>
tc-grps = GOL SOL<br>
<br>
<br>
How many glycerol molecules do you have? If it is only a small<br>
fraction of the system, this treatment of thermostats is likely not<br>
appropriate. See here:<br>
<br>
<a href="http://oldwiki.gromacs.org/index.php/thermostats" target="_blank">http://oldwiki.gromacs.org/index.php/thermostats</a><br>
<br>
<snip><br>
<br>
<br>
===============================================================<br>
Step 0, time 0 (ps) LINCS WARNING<br>
<br>
<br>
The procedure for solving a LINCS warning is always the same.<br>
Identify where things start to fall apart, then verify that your<br>
topology is correct, and your .mdp parameters are reasonable. I've<br>
made a few comments on .mdp parameters above. As for the topology,<br>
that still remains a mystery. Having never used topolbuild, I don't<br>
know how it assigns parameters, so it may work just fine. But in<br>
general, this is always part of the diagnosis.<br>
<br>
-Justin<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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