On 20/09/2012 4:34 PM, Ladasky wrote:
Justin Lemkul wrote
So the initial equilibration was NPT?
Yes.
Justin Lemkul wrote
Did you ever try simply running NVT with
either Berendsen or V-rescale before applying any type of pressure
coupling?
No, I haven't, and I don't remember seeing that described in any work flow.
Point 8 of
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
mentions it.
Justin Lemkul wrote
Immediate application of NPT is often unstable for a variety of reasons,
not
necessarily the temperature coupling algorithm.
All right, that's useful information. But what I am doing here is ripped
from a tutorial file, and modified as little as possible. I try not to
change things that I do not yet understand. My source for the MDP files was
the lysozyme tutorial shell script that accompanied GROMACS 3.3. If there
are procedures in that tutorial that are obsolete, I guess I'm finding that
out the hard way.
Using any single source can lead to problems. Sometimes tutorials are
deliberately stripped down to produce a numerical result in quick time,
but not via a method that is useful for a real problem. Material gets
dated and busy authors don't get paid for keeping them up to date,
unfortunately. Doing all the tutorial material you can find, even if you
think the topic irrelevant, will add do the general knowledge you need.
Further clues can be found in methods reported in published work,
particularly relevant if on systems similar to yours, or by people you
can see are highly experienced with GROMACS because they've published
results from using it for a while.
Mark
Justin Lemkul wrote
Anyone is welcome to contribute to the wiki; it is a community project,
after
all. I would also be interested to see if it can be demonstrated that NPT
with
V-rescale + Berendsen is unstable after an independent NVT simulation with
either method.
I may take the time to try that experiment later. I'll report back with any
findings.
Thanks for your help!
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