[gmx-users] error about pbc
Kieu Thu Nguyen
kieuthu2212 at gmail.com
Mon Jan 28 16:29:44 CET 2013
I reduced time step in equi.mdp file to 20 ps. But the system is still not
balance. Should i continue reduce time step below 20 ps value ? Thanks so
much for any suggestion about appropriate time step value !
Regards,
KT
On Mon, Jan 28, 2013 at 12:53 PM, Kieu Thu Nguyen <kieuthu2212 at gmail.com>wrote:
> 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
>> >>>>> 2500 University Drive NW
>> >>>>> Calgary, AB T2N 1N4
>> >>>>> Canada
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>> >>>>>
>> >>>>> --
>> >>> ==============================****==========
>> >>>
>> >>> Justin A. Lemkul, Ph.D.
>> >>> Research Scientist
>> >>> Department of Biochemistry
>> >>> Virginia Tech
>> >>> Blacksburg, VA
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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
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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