>>>assuming you start from a somewhat artificial
>>>initial set of coordinates, it is probably a
>>>good idea to start the simulation with a fixed
>>>volume and NVT integration, perhaps even using
>>>fix nve/limit with a berendsen thermostat.
You assume correctly. i create something artificial. let me see if i
get it correctly. The volume is fixed with with the xlo,xhi,ylo.yhi if
i use an nvt right?so something like fix 1 all 300 300 0.001 ?
i don't believe that you can RTFM in 10mins. go back and read again.
a look into a text book on "what is an ensemble?" would be extremely
helpful as well.
>>>i would then heat the system for a while at a
>>>higher temperature to remove "residual memory"
>>>of the initial configuration. for efficiency
reasons, you can do this with a fraction of the
system and then use the replicate command to
increase your system.
This can be done with a: fix 1 all heat 1 1.0 ? but i cannot
no. as i wrote before: RTFM!!
understand the while term and what do you mean with the "residual
the is all explained in text books on MD. they typically
give examples of proper equilibration and finite size effects.
then i would switch to
npt (perhaps in combination with the drag parameter)
and bring the system with a slow temperature
gradient to the target temperature and wait
until it has equilibrated.
How someone can see-check the temperature gradient?
i meant a gradient over time. RTFM!!!
Too many questions just for something simple...
because you don't RTFM enough. a mailing list is
no replacement for proper learning of how MD works.
remember that people answering here are all volunteers.
you have to provide something to make it worth answering,
usually you have to feed somebody's curiosity or report
real problems (in the code).
if you are new, you usually get some lenience on simple
questions, but if you use that up quickly, you will soon
be ignored. as far as i am concerned, you are just one
step away from it. quite a lot of what you ask, you could
found out yourself with a little bit common sense, proper
cross-checking of your data and some text book knowledge.