Apologies for replying to myself - maybe I can sharpen up some of my
original questions below:
Reply below
>
>> I am having a problem with my BD simulation either crashing with a Range
>> error or locking up the mdrun process completely.
>>
>> I am running Gromacs 3.3.1 (must use this version ATM because HPC
>> provider has not upgraded yet) on a quad core Intel machine, w/ Fedora
>> Core 7.
>>
>> I have 1000 'particles' in a cubic box (configuration here:
>>
>> http://datavet.hv.se/personal/SK/publicfiles/colloid.pdb
>>
>> where the particles are placed randomly with no two particle centres
>> closer than 4 nm.
>>
>> The particles are defined in the topology here:
>>
>> ; Complete topology file
>> ;
>> ; particles.itp
>>
>> [ defaults ]
>> 1 1 no 1.0 1.0
>>
>> [ atomtypes ]
>> AR 28699.81134 0.00 A 1.0 1.0
>
> Looks like you are using dimensionless eps and sigma while using
> otherwise MD units (e.g. T). Check chapter 2 of the manual. You want to
> multiply your T by boltz (0.008314 or something like that) probably.
Aha! Thank you David.
My goal was to use MD units in everything, since my tabulated data file
was extracted from another GROMACS simulation and is hence already in MD
units (kJ/mol vs. nm), and I would prefer to specify temperatures in K.
My reason for specifying 1.0 for the last two parameters was that I
thought this would allow me to use, unscaled, the tabulated potential
(which is already in MD units).
If I want to do this, what alternative values should I use for the last
two parameters on the [ atomtypes ] line above (given that I am really
only using the g(r) and g''(r) columns to hold my potential data: the
h(r) and h''(r), which I don't care about, are all zeroes) ?
If I change the combination type to 2 or 3 in the [ defaults ] line,
will this remove the unit scaling problem ?
I have checked Chapter 2 in the manual and I am still unsure how to
handle this.
I took your advice (which matches with manual Section 2.4 on *reduced*
units) and scaled my temperature to 2.494353 = 300K * 0.008314. This
did not give a crash, but increasing the timestep and decreasing bd_fric
made the problem return.
Scaling the temperature value in this way did not fix the 'equilibration
around 2x requested temperature' problem mentioned below - g_energy
still shows the temperature settling at a numerical value around 4.988.
Can anyone suggest a reason for this strange thermostat behaviour ?
Many thanks,
Steve Kirk
--
Dr. Steven R. Kirk <[EMAIL PROTECTED], [EMAIL PROTECTED]>
Dept. of Technology, Mathematics & Computer Science (P)+46 520 223215
University West (F)+46 520 223299
P.O. Box 957 Trollhattan 461 29 SWEDEN http://taconet.webhop.org
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