When velocities are assigned randomly, some of that velocity will be along
bond vectors that are constrained and it will be removed by shake. There
are fewer resultin degrees of freedom in the md system than 3 times number
of atoms (-6 for overall rotation and translation). After the first shake
application, temperature should be fine. If it's high longer than that, you
should look into whether the input structure is properly minimized. If it
is coming from md, not minimization, then irest=1 may be a better option.
On Oct 22, 2013 11:57 AM, "Brian Radak" <radak004.umn.edu> wrote:
> This is a somewhat standard feature of using "irest = 0". I don't know why
> this happens and it doesn't appear to happen in the middle of trajectories
> when using "ntt = 2", although they use the same routine as far I know
> (it's also possible that a larger print step just hides that behavior).
>
> Also, I don't think you will see this if, for example, you do a
> non-equilibrium heating using wt namelists and modifying temp0. You can
> also simply discard the first steps (a few 100 ps I guess?) and continue
> with "irest = 1, ntx = 5." Either practice is surely recommended by the
> broader community, although how long of course depends on the particular
> system.
>
> Regards,
> Brian
>
>
>
> On Tue, Oct 22, 2013 at 11:41 AM, Alessandra Lacetera <
> alessandra.lacetera.gmail.com> wrote:
>
> > Hi,
> > I was analysing dynamic simulation results and I've noticed that every
> step
> > of the dynamic starts with a high temperature (more or less 400 K).
> > Consequently also the plot of the potential energy presents a very high
> > fluctuation.
> > These are the parameters I'm using for the dynamic and the plot resulted
> by
> > the simulation.
> >
> > cat << EOF > ${MOL}_md${j}.in
> > PME equil_md
> > &cntrl
> > imin=0, irest=0, ntx=1, ntrx=1,
> > ntt=1, temp0=300.0, tempi = 300.0, gamma_ln=0.0,
> > ntp=1, taup=2.0, vlimit = 20.0,
> > ntb=2, ntc=2, ntf=2,
> > restraint_wt=0.0, restraintmask=':1-143',
> > ibelly=0,
> > nstlim=10000, dt=0.002,
> > ntwe=100, ntwx=1000, ntpr=1000,
> > nmropt=0,
> > jfastw=0, nscm=1000,
> > /
> > &ewald
> > eedmeth=1,skinnb=1.0,dsum_tol=0.000001,
> > /
> > EOF
> >
> > Is it a big deal to start a simulation with a temperature higher than the
> > boiling point of water?
> >
> > I'm attaching here one of the steps of the dynamic
> > Thank you in advance
> >
> > _______________________________________________
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> >
> >
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
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Received on Tue Oct 22 2013 - 10:30:02 PDT
