Hi all,
I have been trying to find out the temperature of a system I ran with AMBER2022 (PMEMD implementation of SANDER, Release 22).
To do so, I obtained the temperature from 3 different ways:
a. temperatures written in the .mden file
b. calculating temperature from the velocities written (using the "temperature" action of cpptraj)
c. calculating temperature from kinetic energy myself, with the kinetic energy obtained using "energy" action of cpptraj (specifically using the ketype vv option, which apparently results in cpptraj "Assuming plus-half time step velocities. Velocities at time 't' will be estimated using force info")
I am a bit perplexed to find that the temperature obtained as described above all differ from each other.
with a. giving an average temperature of ~333 K, b. giving an average temperature of ~342 K and c. giving an average temperature of ~ 344 K
So I am wondering how should I obtain temperature of my system?
Also how is the temperature written in the .mden file actually determined and why does it differ from the temperature obtained with the other ways so significantly ?
===below is the run control (mdin) details of my simulation===
barostat=1,
imin=0, ntx=1, irest=0,
ntpr=500, ntwr=50000, ntwx=500, ntwv=-1, ntwe=500, ntwf=-1
ntf=2,ntb=2, nsnb=5,cut=10.0,
nstlim=500000, nscm=100, t = 0.00000, dt = 0.002, vlimit = 0.
ntt=1, ig=-1, temp0 = 333.00000, tempi = 333, tautp= 0.1,
ntp = 3, pres0 = 1.00000, comp = 46.00000, taup = 1.0000
csurften = 3, gamma_ten = 0.00000, ninterface = 2,
ntc=2, jfastw=0, tol=0.0004,
ene_avg_sampling=100,
&end
&ewald
ew_type= 0,
nbflag=0,
vdwmeth=0,
eedmeth=1,
netfrc=1,
&end
===================================================
Regards,
Zihan
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Received on Tue Jul 16 2024 - 23:30:02 PDT
