I can't tell you if there is a problem or not.
The only intended difference that I can see is that for 4.5.X:
# grompp by default sets the new nsttcouple parameter equal to
nstlist, this means T-coupling is done less frequently; grompp checks
if tau_t is large enough
# grompp by default sets the new nstpcouple parameter equal to
nstlist, this means P-coupling is done less frequently; grompp checks
if tau_p is large enough
(see http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x )
Note that there were some fixes to P-R scaling in the 4.0.X series --
se http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0
To test this further, I suggest that you need to define a good
procedure to ensure that what you are seeing is (b) from a well
equilibrated system and is also (b) statistically significant.
I suggest that one way to do this is to cycle through your T- and P-
coupling options at a given temperature. For example, at T=500 K, run
X ns of Berendsen, then X ns of Parrinello-Rahman, then back to
Berendsen, and so on for a few cycles. Each time you switch coupling
method, be sure to use the structure output from the previous run.
Also be sure that X ns is as long as you can afford. This way, you
will be able to pick out systematic changes as temperature/density
oscillations with periods that are related to your changes of
algorithm. This also ensures that what you are seeing is not simply an
artifact of having a poorly equilibrated density in your initial
structure.
You could also run the same cycle with Berendsen and V-rescale.
Chris.
-- original message --
Dear gmxers,
According to my recent practice, we find that the Berensen methods
for T- and P- coupling can yield reasonable averaged density as a
function of temperature, but when the v-rescale method and the
Parrinello-Rahman method are employed for T- and P- coupling, somewhat
unexpected results (i.e. density at higher temperature is bigger than
that at lower tempearature) are obtained. Generally, the latter setup
is considered to be prefered to the former one in simulating realistic
ensemble. I am using gmx-4.5.3, and previously I have also performed
one similar work using 4.0 which can generate expected results using
the latter setup. I wonder if this version 4.5.3 has some bugs in
calculating T and P, and are they dealt with in 4.5.4? Please give me
some hints.
Yours sincerely,
Chaofu Wu, Dr.
------------------
Department of Chemistry and Materials Science, Hunan University of
Humanities, Science and Technology, Loudi 417000, the People?s
Republic of China (P.R. China)
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