[gmx-users] error about pbc
Kieu Thu Nguyen
kieuthu2212 at gmail.com
Sun Jan 27 18:15:12 CET 2013
@Justin,
Fmax=8.0226669e+00
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
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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