grivet wrote:
Le mardi 30 mars 2010 à 12:26 -0400, Justin A. Lemkul a écrit :
Having cleared the first hurdle, I ran mdrun for steepest descent (5832
molecules). The program stopped after 2067 steps, with maximum force =
1.58E02 on atom 4870. How important is that warning?
What warning? This one?
http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
I wanted to know what maximum force was acceptable at this stage of the
computation.
Sure, as the link I provided should have indicated. My question was that you
made reference to a warning, but provided no information that indicated any
warning at all. Fmax of 158 should be fine.
The volume and density evolved rather smoothly to reasonable values. I
have two values for the density; according to the .log file, it is
0.9937E03 and according to g_energy, it is 1.015E03; which should I
believe?
Probably g_energy. See the manual, Appendix C. How many values in the .log
file are you looking at? Anything printed there is just an instantaneous value,
and may not represent the actual average over the simulation.
You're right; both give identical averages.
rlist, rcoulomb and rvdw were all set to 1.0; is that reasonable ?
For a simple system of water, yes, probably. Understand though that force field
parameter sets generally have recommended (required) cutoffs for which the force
field was designed to be accurate. Deviations are not recommended unless you
can justify doing so. For example, with PME, the value of rcoulomb is somewhat
flexible, but the same is not always true for other cutoffs.
In any case, it is always recommended to read the primary literature for the
parameterization of the force field or specific molecule parameters. Just
yesterday, there was a thread with several posted references about comparing
water models. You might find some useful background reading there as to what's
considered "reasonable" for different scenarios.
-Justin
Thank you for your time and help
JP Grivet
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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