AMBER Archive (2007)

Subject: Re: AMBER: abnormal high temperature during NPT ensembles MD

From: ebright HMS (amber.hms_at_gmail.com)
Date: Wed Feb 28 2007 - 10:29:41 CST

hi, Carlos:

It seems stable at NVT. But whenever I run it at NPT, it complains the
following after a few ps steps,
----------------------------------------------------
vlimit exceeded for step 21297 ; vmax = 178.029715000357

     Coordinate resetting (SHAKE) was not accomplished
     within 3000 iterations

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.
--------------------------------------------------------

Thanks !

ebright

On 2/27/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
>
> perhaps it is the parameters?
> was it stable for simulations at NVT?
>
> On 2/27/07, ebright HMS <amber.hms_at_gmail.com > wrote:
> >
> > hi all :
> >
> > I am simulating a small organic molecule (coumarin-like ) in explicit
> > water
> > solvent by Amber 8. 1ns NVT ensemble equilibration run was first
> > conducted to make
> > sure the system equilibrate under constant volume. However, I observed
> > very abnormal high temperature (above 400K) in the followed NPT ensemble
> >
> > production run although I set the temperature at 300K. It seems that the
> > system
> > is 'boiling' somehow. Can anybody give me some inputs why this happens ?
> >
> > Thanks ! I listed the production run input and output below.
> > Additionally, I am
> > not able to set the cut-off at 10 or 12 since it always complains "
> > Ewald PARAMETER
> > RANGE CHECKING: out of legal range".
> >
> >
> > md3.in
> > ------------------------
> > NPT production MD
> > &cntrl
> > imin = 0, irest = 1, ntx = 5,
> > ntb = 2, pres0 = 1.0, ntp = 1,
> > taup = 2.0,
> > cut = 8, ntr = 0,
> > ntc = 2, ntf = 2,
> > tempi = 300.0, temp0 = 300.0,
> > ntt = 3, gamma_ln = 1.0,
> > nstlim = 100000, dt = 0.002,
> > ntpr = 100, ntwx = 500, ntwr = 1000
> > /
> > END
> >
> > md3.out
> > -------------------------------------------------------------------------------------------------
> >
> > check COM velocity, temp: 0.017613 0.47(Removed)
> >
> > NSTEP = 13000 TIME(PS) = 1226.000 TEMP(K) = 626.92 PRESS =
> > 7428.4
> > Etot = -1117.9956 EKtot = 1337.9965 EPtot = -
> > 2455.9921
> > BOND = 3.8632 ANGLE = 8.2509 DIHED =
> > 4.8641
> > 1-4 NB = 6.6715 1-4 EEL = -32.0330 VDWAALS =
> > 507.9005
> > EELEC = -2955.5094 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 462.0735 VIRIAL = -1360.9398 VOLUME =
> > 11366.1939
> > Density =
> > 0.9452
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu