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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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
================================ 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
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Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Tue Oct 22 2013 - 09:00:05 PDT
