[gmx-users] error about pbc

Justin Lemkul jalemkul at vt.edu
Mon Jan 28 16:34:16 CET 2013



On 1/28/13 10:29 AM, Kieu Thu Nguyen wrote:
> 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 !
>

The first step I would take is to keep halving the time step until the system is 
stable, then increase to the desired value after you've achieved a stable system.

-Justin

> 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
>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<
>>> http://vt.edu/Pages/Personal/justin>
>>>>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>>>>>
>>>>>>
>>>>>> ==============================****==========
>>>>>>
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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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>>
>>

-- 
========================================

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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