Hi GROMACS user group!
Maybe this should be aimed at the developers' mailing list... Anyway, I've been
having some problems (blowing up) when I tried to simulate a molecule such that
one part is coupled to a thermal bath using SD, and another part is not coupled
to any bath. Effectively, the uncoupled part has infinite "relaxation time"
(tau-T) which is the same as zero coupling (gamma); however, in the *.mdp file
it is unrealistic to put in the value infinity for the tau-T parameter. The 4.0
manual specifically says, in section 7.3.14, "Temperature coupling":
tau t: [ps]
time constant for coupling (one for each group in tc grps), 0 means no
temperature coupling
However, when I tried putting in zero I got the following (debugging
information log-file)
line 267: SD const tc-grp 0: b nan c inf d -inf
line 268: SD const tc-grp 1: b 2.08438e-14 c 8.33021e-11 d -2.5e-07
where group 0 had tau-T[0] = 0 and group 1 had tau-T[0] = 1 ps . This shows
that when I put zero in the temperature coupling timescale (for SD this is not
exactly a first-order relaxation time), the SD parameters blow up.
Note that when I put tau-T[0] = 1000 or tau-T[0] = 10000, the simulation ran
properly.
Where in the code can I check that what is written in the manual is, indeed
correct?
(i.e., I expect an if statement saying that if the tau-T value of some
temperature coupling group is zero, then take the inverse of that to be
effectively zero).
Thanks in advance,
--
Inon Sharony
ינון שרוני
+972(3)6407634
atto.TAU.ac.IL/~inonshar
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