[gmx-users] equilibration + Segmentation fault
Justin A. Lemkul
jalemkul at vt.edu
Sat Jun 5 04:46:47 CEST 2010
Nilesh Dhumal wrote:
> I am using the opls parameters from Lope's paper.
> In vaccum energy minimzatin is working well. MD is not at all working.
> My other systems are running well. In the present system I changed the
> anion, cation parameters are fine.
> Is the problem with anion parameters?
If it's something you've changed, and all the other components are working, then
yes, I would suspect that there's likely a problem with whatever you've changed.
Please do consult the link I posted - it contains a "greatest hits" of sorts
of the most useful advice I can come up with for diagnosing unstable systems.
> On Fri, June 4, 2010 10:20 pm, Justin A. Lemkul wrote:
>> Nilesh Dhumal wrote:
>>> I am trying to equilibrate my system, ionic liquids. My simulations
>>> gets stop immediately. I reduced the step size. I modified initial
>>> structure. I changed the box size. I checked force field parameters. I
>>> am using opls foce field. I repeated my energy minimization 2-3 times. I
>>> could not solve the problem. Every time i am geting following error
>>> step 0Warning: 1-4 interaction between 20 and 27 at distance 3.803
>>> which is larger than the 1-4 table size 2.400 nm These are ignored for
>>> the rest of the simulation This usually means your system is exploding,
>>> if not, you should increase table-extension in your mdp file or with user
>>> tables increase the table size Segmentation fault
>>> Can you tell me how to solve this problem.
>> Please consult the following:
>> The prime suspect in my mind is your topology. How have you validated
>> the parameters for your ionic liquids? Does in vacuo minimization and
>> short MD of each component separately run stably? While OPLS is quite
>> versatile, parameterizing ionic liquids properly is not a trivial task,
>> and is probably not very straightforward.
>>> Here I have pasted the eqilibration file.
>>> title = cpeptid position restraining cpp
>>> = /usr/bin/cpp
>>> constraints = none integrator = md dt
>>> = 0.001 ; ps !
>>> nsteps = 100000 ; total 1.0 ps. nstcomm =
>>> nstxout = 10000 nstvout = 10000 nstfout
>>> = 0
>>> nstlog = 10 nstenergy = 10 nstlist =
>>> ns_type = grid rlist = 1.0 coulombtype
>>> = PME
>>> vdwtype = cut-off rcoulomb = 1.0 rvdw
>>> = 1.4
>>> fourierspacing = 0.12 fourier_nx = 0 fourier_ny
>>> = 0
>>> fourier_nz = 0 pme_order = 4 ewald_rtol =
>>> optimize_fft = yes ; Berendsen temperature coupling is on
>>> Tcoupl = v-rescale
>>> tau_t = 0.1 tc-grps =system ref_t = 300 ; Pressure coupling is on
>>> Pcoupl = parrinello-rahman
>>> pcoupltype = isotropic tau_p = 0.5 compressibility
>>> = 4.5e-5
>>> ref_p = 1.0 ; Generate velocites is on at 300 K.
>>> gen_vel = yes gen_temp = 300.0 gen_seed
>>> = 173529
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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