Hi Brandon,
See $AMBERHOME/test/4096wat/Run.pure_wat_nmr_temp_reg for an example:
short md, nvt ensemble
&cntrl
ntx=1, irest=0,
ntc=2, ntf=2, tol=0.0000001,
nstlim=20, ntt=3, gamma_ln=1000,
ntpr=1, ntwr=0,ntwx=0,
dt=0.001,nmropt=1,
/
&ewald
nfft1=50, nfft2=50, nfft3=50,
/
&wt type='TEMP0', istep1=0, istep2=10,
value1=0.0, value2=30.0 /
&wt type='TEMP0', istep1=11, istep2=20,
value1=30.0, value2=0.0 /
&wt type='END' /
It is a pretty simple concept. You just set the start step and end step that
you want to linearly scale the target variable over and what you want it to
start at and end at. Essentially you set nmropt=1 and then include the &wt
section.
The calculation stopping at 3500 is unrelated to the temperature. It looks
to me like something is killing the job. Do you have a timelimit for
interactive jobs on your machine? Are you logging out and that is killing
the job? Do you have enough disk space? You should try nohupping the job and
see if it keeps running:
nohup $AMBERHOME/bin/sander -O -i ... &
All the best
Ross
> -----Original Message-----
> From: Brandon Sim [mailto:simpavid.gmail.com]
> Sent: Friday, June 29, 2012 3:06 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] sander termination upon reaching end temperature
>
> Dear Carlos:
>
> I was indeed attempting to 'heat' the system for equilibration:
> following
> Ross Walker's tutorial here (
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/secti
> on5.htm
> )
>
> Can you advise on a tutorial that includes the weight change you
> mention?
>
> Also, the end of the sander out file:
>
>
> NSTEP = 3400 TIME(PS) = 6.800 TEMP(K) = 299.60 PRESS =
> 0.0
> Etot = -65442.0643 EKtot = 15593.5184 EPtot =
> -81035.5827
> BOND = 548.0896 ANGLE = 1468.0511 DIHED =
> 1956.8259
> 1-4 NB = 666.6706 1-4 EEL = 6764.4623 VDWAALS =
> 8890.0799
> EELEC = -101329.7622 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.4759E-04
> ----------------------------------------------------------------------
> --------
>
>
> NSTEP = 3500 TIME(PS) = 7.000 TEMP(K) = 299.54 PRESS =
> 0.0
> Etot = -65512.8173 EKtot = 15590.1215 EPtot =
> -81102.9388
> BOND = 559.2555 ANGLE = 1529.1253 DIHED =
> 1927.5384
> 1-4 NB = 659.7034 1-4 EEL = 6719.2474 VDWAALS =
> 8818.1655
> EELEC = -101315.9743 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.6503E-04
> ----------------------------------------------------------------------
> --------
>
> That is all there is - there is no end summary or anything like that.
>
> The mdinfo file contains only this last printout (nstep=3500)
>
> Thanks,
> Brandon
>
> On Fri, Jun 29, 2012 at 6:42 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > seems ok- but be aware that this is NOT going to be gradual heating.
> > you've assigned a thermostate of 300K, which means the T will go to
> > 300K very quickly. if you want to heat 0-300K, you need to slowly
> > change temp0. tempi just sets initial temperature and the thermostat
> > kicks in immediately.
> >
> > can you paste the end of the sander mdout- from the last energy
> report
> > to the end?
> >
> > On Fri, Jun 29, 2012 at 6:39 AM, Brandon Sim <simpavid.gmail.com>
> wrote:
> > > Initial MD equilibration: 20 ps, at constant volume, 0-300 K
> > > &cntrl
> > > imin=0,
> > > irest=0,
> > > ntx=1,
> > > igb=0,
> > > scee=1.2,
> > > ntb=1,
> > > cut=10,
> > > nstlim=10000,
> > > dt=0.002,
> > > ntc=2,
> > > ntf=2,
> > > ntt=3,
> > > gamma_ln=1.0,
> > > tempi=0.0,
> > > temp0=300.0
> > > ntpr=100,
> > > ntwx=100,
> > > /
> > >
> > > On Fri, Jun 29, 2012 at 6:24 AM, Carlos Simmerling <
> > > carlos.simmerling.gmail.com> wrote:
> > >
> > >> can you reply with a copy/paste of your input file?
> > >>
> > >> On Fri, Jun 29, 2012 at 6:14 AM, Brandon Sim <simpavid.gmail.com>
> > wrote:
> > >> > Dear Vishal,
> > >> >
> > >> > Sorry - I mistyped. I meant 7 picoseconds (i have timestep of
> 0.002
> > >> > picoseconds with SHAKE on).
> > >> >
> > >> > Has this problem occurred before to anyone?
> > >> >
> > >> > By the way, the .mdcrd file wrote was written out in the
> appropriate
> > >> > format, with box size at the end, anyway..
> > >> >
> > >> > On Fri, Jun 29, 2012 at 5:46 AM, Vishal Kumar Jaiswal
> > >> > <vishal3990.gmail.com>wrote:
> > >> >
> > >> >> Hi Brandon
> > >> >>
> > >> >> No this is not the expected behavior ,the simulation should
> complete
> > the
> > >> >> number of steps ( nstlim)
> > >> >> By the way, with 3500 steps you are covering 7 nanoseconds
> which
> > >> means a
> > >> >> step size of 2 picoseconds. i do not think it is acceptable.
> > >> >> you should have timestep of 0.002 picoseconds ( if you restrict
> > hydrogen
> > >> >> movement by SHAKE , NTC = 2) or else use timestep of 0.001
> > picosecond.
> > >> >>
> > >> >> Hope this helps
> > >> >>
> > >> >> Vishal
> > >> >>
> > >> >> On Fri, Jun 29, 2012 at 11:17 AM, Brandon Sim
> <simpavid.gmail.com>
> > >> wrote:
> > >> >>
> > >> >> > Dear Amber users,
> > >> >> >
> > >> >> > Does sander stop equilibration when temp0 is reached, even
> when the
> > >> >> number
> > >> >> > of steps has not gotten to nstlim?
> > >> >> >
> > >> >> > I ran three simulations with nstlim=10000, but all three
> ended at
> > step
> > >> >> > 3500, resulting in 7 nanoseconds of trajectory and 35 frames
> (I
> > wrote
> > >> a
> > >> >> > frame each 100 steps).
> > >> >> >
> > >> >> > The temperature had already gotten to ~300 K , which was my
> temp0.
> > Is
> > >> >> this
> > >> >> > expected behavior, is my script wrong somewhere?
> > >> >> >
> > >> >> > Thanks,
> > >> >> > Brandon
> > >> >> > _______________________________________________
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Received on Fri Jun 29 2012 - 15:30:02 PDT
