[gmx-users] error about pbc
Kieu Thu Nguyen
kieuthu2212 at gmail.com
Mon Jan 28 06:53:02 CET 2013
Thank Justin and Tsjerk so much for your help !
I will try smaller time step. And i hope it work :-)
Regards,
KT
On Mon, Jan 28, 2013 at 10:19 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:
> Well, 20-30 fs is fine with Martini. But you may have to take care
> initially, and start with a smaller time step.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Jan 28, 2013 at 3:11 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote:
> >
> >> @Justin,
> >> Fmax=8.0226669e+00
> >>
> >
> > OK, that looks good.
> >
> >
> > the system includes protein, lipid, water, ion Cl-
> >>
> >> em.mdp file is
> >>
> >> integrator = steep
> >> tinit = 0.0
> >> dt = 0.02
> >> nsteps = 50000
> >> nstcomm = 1
> >> nstxout = 5000
> >> nstvout = 5000
> >> nstfout = 0
> >> nstlog = 1000
> >> nstenergy = 1000
> >> nstxtcout = 1000
> >> xtc_precision = 1000
> >> nstlist = 1
> >> ns_type = grid
> >> pbc = xyz
> >> rlist = 1.4
> >> coulombtype = Shift
> >> rcoulomb_switch = 0.0
> >> rcoulomb = 1.2
> >> epsilon_r = 15
> >> vdw_type = Shift
> >> rvdw_switch = 0.9
> >> rvdw = 1.2
> >> DispCorr = No
> >> tcoupl = no
> >> pcoupl = no
> >> gen_vel = no
> >> constraints = none
> >> constraint_algorithm = Lincs
> >> continuation = no
> >> lincs_order = 4
> >> lincs_warnangle = 30
> >>
> >>
> >> equi.mdp file is
> >>
> >> integrator = md
> >> tinit = 0.0
> >> dt = 0.03
> >>
> >
> > Does a smaller time step work? I know the whole point of a MARTINI
> > simulation is to use a 20-40 fs time step, but in my (very very limited)
> > experience, nothing over 20 fs is consistently stable. Perhaps others
> with
> > better experience can offer pointers.
> >
> > -Justin
> >
> >
> > nsteps = 3000000
> >> nstcomm = 1
> >> comm-grps =
> >> nstxout = 5000
> >> nstvout = 5000
> >> nstfout = 0
> >> nstlog = 1000
> >> nstenergy = 1000
> >> nstxtcout = 1000
> >> xtc_precision = 100
> >> xtc-grps =
> >> energygrps =
> >> nstlist = 10
> >> ns_type = grid
> >> pbc = xyz
> >> rlist = 1.2
> >> coulombtype = Shift
> >> rcoulomb_switch = 0.0
> >> rcoulomb = 1.2
> >> epsilon_r = 15
> >> vdw_type = Shift
> >> rvdw_switch = 0.9
> >> rvdw = 1.2
> >> DispCorr = No
> >> tcoupl = Berendsen
> >> tc-grps = Protein DSPC Ion_W
> >> tau_t = 1.5 1.5 1.5
> >> ref_t = 310 310 310
> >> Pcoupl = Berendsen
> >> Pcoupltype = semiisotropic
> >> tau_p = 3.0 3.0
> >> compressibility = 3e-4 3e-4
> >> ref_p = 1.0 1.0
> >> gen_vel = no
> >> constraints = none
> >> constraint_algorithm = Lincs
> >> continuation = no
> >> lincs_order = 4
> >> lincs_warnangle = 30
> >>
> >> Thanks so much for any help !
> >> Regards,
> >> KT
> >>
> >>
> >> On Sun, Jan 27, 2013 at 8:26 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >>
> >>>
> >>> On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote:
> >>>
> >>> Thank Tsjerk so much !
> >>>> But after being minimized 50000 steps and equilibrated 90 ns, there
> are
> >>>> some bonds in the system that rotate more than 30 degrees.
> >>>> I applied tips for blew up system as you advised. But the system does
> >>>> not
> >>>> achieve balance.
> >>>> Should i carry out more many steps for minimization ? or minimize many
> >>>> times ? to get more equilibrated system.
> >>>>
> >>>>
> >>>> I would say that 50000 steps of minimization is far more than is
> >>> normally
> >>> necessary. What Fmax do you achieve at the end of EM? What is in the
> >>> system? What is in your .mdp file? Systems can randomly crash if the
> >>> model
> >>> physics breaks due to incorrect .mdp settings or an unstable topology.
> >>>
> >>> -Justin
> >>>
> >>>
> >>> On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar <
> tsjerkw at gmail.com
> >>>
> >>>> wrote:
> >>>>>
> >>>>
> >>>> Hi KT,
> >>>>
> >>>>>
> >>>>> This is caused by another problem. Your system blew up. Check
> messages
> >>>>> before this one, and check the log for LINCS warnings.
> >>>>>
> >>>>> Cheers,
> >>>>>
> >>>>> Tsjerk
> >>>>>
> >>>>> On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen <
> >>>>> kieuthu2212 at gmail.com
> >>>>>
> >>>>> wrote:
> >>>>>>
> >>>>>>
> >>>>> Dear All,
> >>>>>
> >>>>>>
> >>>>>> My MD simulation has an error
> >>>>>>
> >>>>>> Warning: Only triclinic boxes with the first vector parallel to the
> >>>>>>
> >>>>>> x-axis
> >>>>>
> >>>>> and the second vector in the xy-plane are supported.
> >>>>>> Box (3x3):
> >>>>>> Box[ 0]={ nan, nan, nan}
> >>>>>> Box[ 1]={ nan, nan, nan}
> >>>>>> Box[ 2]={ nan, nan, nan}
> >>>>>> Can not fix pbc.
> >>>>>>
> >>>>>> I searched on Gromacs-errors web, but i did not see this error.
> >>>>>> How can i fix it ?
> >>>>>>
> >>>>>> Thanks and regards,
> >>>>>> KT
> >>>>>> --
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> >>>>> --
> >>>>> Tsjerk A. Wassenaar, Ph.D.
> >>>>>
> >>>>> post-doctoral researcher
> >>>>> Biocomputing Group
> >>>>> Department of Biological Sciences
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> >>>>> --
> >>> ==============================****==========
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Research Scientist
> >>> Department of Biochemistry
> >>> Virginia Tech
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> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
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> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Biocomputing Group
> Department of Biological Sciences
> 2500 University Drive NW
> Calgary, AB T2N 1N4
> Canada
> --
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