[gmx-users] Different temperature

[Mark Abraham]

Andrea Carotti wrote:
> Hi all,
> sorry for the long message.
> I'm performing an MD on a system made by a protein and water. I use the 
> gromos96 ff.

<snip>

> As you can see the temperature increase rapidly to a value near 350K. 
> Could you please explain me the problem (if it's a problem) and point me 
> out some suggestions to solve it?

What did you do to the system before this?

Ordinarily something along the lines of
1) energy minimization to relieve bad contacts after solvation, followed by
2) (optionally position-restrained) NVT simulation(s) to equilibrate 
temperatures, followed by
3) (optionally position-restrained) NPT simulation(s) to equilibrate P 
while T is already pretty good
leads to sensibly equilibrated systems, but your mileage will vary with 
your system, of course.

Find some recent MD papers you think relevant/analogous to your system 
and copy them, if you think they did something reasonable here.

Mark