well I will have to end up in the NPT though - your reason for NVT is that
speed?
On Thu, Apr 13, 2017 at 7:57 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Normally I'd run NPT until volume equilibrates as a first step towards a
> starting ensemble, see the literature for what people call equilibrated
> these days. Once volume has equilibrated, you can switch to NVT.
>
>
> On 4/12/17 10:41 PM, Jorgen Simonsen wrote:
> > Thanks - just to clarify I have followed some of these tutorial on the
> > heating( http://ambermd.org/tutorials/advanced/tutorial8/loop7.htm) I am
> > not sure how to gradually heat the system then - could u provide a link
> or
> > some key words I would be able to look into? I would like to increase the
> > temperature of the system e.g. 50 K for each 10 ps.
> >
> > So the system might not to well equilibrated af the 100 ps so would you
> > recommend me to run additional 100 ps in the NPT before starting to
> > initiate the simulations with new seeds?
> >
> > Thanks
> >
> >
> >
> > On Thu, Apr 13, 2017 at 7:15 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> I don't see any gradual warming - your first run doesn't slowly heat,
> >> and your final run starts with irest=0 so no velocities.
> >>
> >> Bill
> >>
> >>
> >> On 4/12/17 10:03 PM, Jorgen Simonsen wrote:
> >>> Hi all,
> >>>
> >>> I am having an issue with the temperature after I have slowly heated up
> >> the
> >>> system:
> >>>
> >>> 100ps MD with res on protein
> >>>
> >>> &cntrl
> >>>
> >>> imin = 0,
> >>>
> >>> irest = 0,
> >>>
> >>> ntx = 1,
> >>>
> >>> ntb = 1,
> >>>
> >>> cut = 10.0,
> >>>
> >>> ntr = 1,
> >>>
> >>> ntc = 2,
> >>>
> >>> ntf = 2,
> >>>
> >>> tempi = 0.0,
> >>>
> >>> temp0 = 300,
> >>>
> >>> ntt = 3,
> >>>
> >>> gamma_ln = 1.0,
> >>>
> >>> nstlim = 50000, dt = 0.002
> >>>
> >>> ntpr = 5000, ntwx = 5000, ntwr = 5000
> >>>
> >>> /
> >>>
> >>> Keep protein fixed with weak restraints
> >>>
> >>> 50.0
> >>>
> >>> RES 1 40
> >>>
> >>> END
> >>>
> >>> END
> >>>
> >>>
> >>>
> >>> I use the sander.MPI
> >>>
> >>>
> >>> mpirun -np 16 ~/amber14/bin/sander.MPI -O -i md_disulfides.in -p
> >>> solv.prmtop -c heat.rst -r md.rst
> >>>
> >>>
> >>> with the following md input file:
> >>>
> >>>
> >>> 10ps MD
> >>>
> >>> &cntrl
> >>>
> >>> imin = 0, irest = 0, ntx = 1, iwrap=1,
> >>>
> >>> ntb = 2, pres0 = 1.0, ntp = 1,
> >>>
> >>> taup = 2.0,ig=-1,
> >>>
> >>> cut = 10.0, ntr = 0,
> >>>
> >>> ntc = 2, ntf = 2,
> >>>
> >>> tempi = 300, temp0 = 300,
> >>>
> >>> ntt = 3, gamma_ln = 1.0,
> >>>
> >>> nstlim = 10000000, dt = 0.002,
> >>>
> >>> ntpr = 5000, ntwx = 5000, ntwr = 5000
> >>>
> >>> /
> >>>
> >>> I do want to start from random seeds to get indenpendent runs so I set
> >> the
> >>> ig=-1 but still I would expect to be close to the equilibrated system.
> >>>
> >>> but from the first round I get the following error/ warning
> >>>
> >>>
> >>> NSTEP = 0 TIME(PS) = 100.000 TEMP(K) = 440.42 PRESS =
> >>> -621.5
> >>>
> >>> Etot = -19730.8465 EKtot = 8077.7368 EPtot =
> >>> -27808.5832
> >>>
> >>> BOND = 105.8078 ANGLE = 205.4744 DIHED =
> >>> 473.4839
> >>>
> >>> 1-4 NB = 130.7175 1-4 EEL = 2395.4889 VDWAALS =
> >>> 3606.5258
> >>>
> >>> EELEC = -34726.0816 EHBOND = 0.0000 RESTRAINT =
> >>> 0.0000
> >>>
> >>> EKCMT = 2504.5210 VIRIAL = 4159.2641 VOLUME =
> >>> 123313.0860
> >>>
> >>> Density =
> >>> 0.7475
> >>>
> >>> Ewald error estimate: 0.6640E-04
> >>>
> >>> ------------------------------------------------------------
> >> ------------------
> >>>
> >>> ***** Processor 0
> >>>
> >>> ***** System must be very inhomogeneous.
> >>>
> >>> ***** Readjusting recip sizes.
> >>>
> >>> In this slab, Atoms found: 1415 Allocated: 1412
> >>>
> >>>
> >>> any help appreciated - thanks!
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 12 2017 - 23:30:02 PDT
