[gmx-users] error about pbc
Tsjerk Wassenaar
tsjerkw at gmail.com
Mon Jan 28 04:19:23 CET 2013
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
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
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>>> >
>>>
>>> ==============================****==========
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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<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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