On Wed, Jul 17, 2024, Zihan Zhou via AMBER wrote:
>
>I have been trying to find out the temperature of a system I ran with
>AMBER2022 (PMEMD implementation of SANDER, Release 22).
Some followups on earlier comments:
You don't say how many snapshots you used to get an average temperature. It
looks like maybe only 1000 steps (based on ntwx and nstlim), which might be
too few.
>ntt=1, ig=-1, temp0 = 333.00000, tempi = 333, tautp= 0.1,
This is quite a poor choice of thermostat, at least for most systems. The
Berendsen thermostat is old, but the main problem is with a tautp value of
0.1, which is really short. Consider using ntt=3, or at least a value of
tautp that is 10 to 100 times larger.
The mdout file will show you both the average temperature and it
fluctuations about the average. Try different thermostats, with a smaller
value of ntpr, and see what differences you get.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 17 2024 - 12:00:02 PDT
