[gmx-users] error about pbc

Justin Lemkul jalemkul at vt.edu
Mon Jan 28 03:11:51 CET 2013



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
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
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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://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

========================================



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