[gmx-users] water box with prescribed volume and density

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 1 16:18:17 CEST 2010

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.


> Thank you for your time and help
> JP Grivet


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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