[gmx-users] Re: v-rescale
Peter C. Lai
pcl at uab.edu
Thu Sep 20 09:23:46 CEST 2012
On 2012-09-20 12:18:02AM -0700, Ladasky wrote:
> Hi Peter,
> Thanks for your response.
> Rather than dragging this thread too far off-topic, I'll direct you back to
> my thread, where I have just posted additional details. I took a warning
> message from GROMACS a bit too literally and it caused me to use conditions
> that blew up my simulations.
> I am interested in your protocol for "the typical equilibration." If this
> is in fact standardized, do you have a reference? It doesn't match up with
> anything in the tutorial files I have been using to run my own simulations.
> Admittedly, those files are from GROMACS 3.3, and the procedures may be a
> bit out of date.
Generally it's probably not a good idea to rely on tutorials designed
around 3.3 when a google search for gromacs tutorial shows a series of 4.5.x
tutorials written by Justin himself, with explanations of why certain steps
are conducted. (also when certain features may be implemented differently,
such as the introduction of the v-rescale thermostat).
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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