Thank you Mark for your response,
In carrying out the test you recommended I realised that I had set the
integrator to sd, in such a case the tcoupl parameter is ignored. This explains
my well behave temperature in the absence of setting a tcoupl option. When I
wrote the input file original
Dear All,
I had intended to perform an NPT simulation, however
although I selected a barostat I omitted to select a thermostat,
nevertheless I did set tc_grps= system, tau_t = 0.1 and ref_t= 300. My
temperature appears to fluctuate around the desired 300 K. My question
is, by setting tau_t
Dear All,
I had intended to perform an NPT simulation, however although I selected a
barostat I omitted to select a thermostat, nevertheless I did set tc_grps=
system, tau_t = 0.1 and ref_t= 300. My temperature appears to fluctuate around
the desired 300 K. My question is, by setting tau_t and
Dear all,
Lennard Jones radius parameters are converted between gromacs and amber with
the conversion factor (2**(5/6))/10 in the amb2gmx script. While I understand
that the 10 takes care of the Angstrom to nanometers conversion I do not
understand the origin of the 2 to the power of 5/6. I wou
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