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/section5.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
