Just to follow up on what Carlos said, make sure when you are
calculating temperature in Cpptraj you're using the same value for
SHAKE (ntc) as was used in the simulation (in this case 'ntc 2').
-Dan
On Wed, Jul 17, 2024 at 6:50 AM Carlos Simmerling via AMBER
<amber.ambermd.org> wrote:
>
> The temperature in mdin is the target T of the thermostat.
> When you use the KE or velocities, you need to ask use the correct number
> of degrees of freedom. This must account for use of shake. You didn't
> mention if you did this or not.
> Also I see you are using the Berendsen thermostat with quite weak coupling.
> This model is less commonly used these days.
> Also you don't mention the temperature reported in the mdout, which is the
> most direct way to get what you want.
>
> On Wed, Jul 17, 2024, 2:21 AM Zihan Zhou via AMBER <amber.ambermd.org>
> wrote:
>
> > 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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> >
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Received on Wed Jul 17 2024 - 07:00:01 PDT
