Dear Ross,
Thanks for your example.
In the example you provided, am I understanding it correctly by thinking
that it sets the bath temperature temp0 to 30 K after 10 steps, then cools
it back down to 0 K from steps 11-20?
I think that something must have been killing the job after step 3500, as
it worked the second time I tried it.
Thanks,
Brandon
On Fri, Jun 29, 2012 at 6:23 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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 Sat Jun 30 2012 - 15:30:03 PDT
