[gmx-users] Warning: 1-4 interaction
Moeed
lecielll at googlemail.com
Sun Mar 6 02:18:55 CET 2011
Hello Justin,
I just scanned through the manual and also looked into the list to learn
about the significance of reciprocal part to realize your statement. I did
not find much about the fact that how I can judge if fourierspacing is the
cause of the crash (I mean relevance between fourierspacing and coulb
recip). I suspect the cause of crashes is because of electrostatics
settings. BEfore that I had only vdw no run crashed. Since I used to get
LINCS warning I removed bond constraints but still system is showing
instabilities. I am confident that topology is fine and just wondering how
else one can inspect root cause for unphysical forces.
fourierspacing =0.12 : Coul. recip. 636.217 8.69433
8.62908 0.0167398 3.68278
fourierspacing =0.3 : Coul. recip. 642.921 6.06063
6.02832 -0.00984063 -2.16496
>>
> Everything has a cause; nothing is accidental. No stable run should ever
> show LINCS warnings like this, so yes, there is something to fix.
>
> You also have not proven that your fourierspacing is not the cause. The
> proper term to analyze is Coul-recip, which corresponds to reciprocal space
> Coulombic term. I don't see that listed below.
>
> -Justin
>
>
> Thanks,
>> Best,
>> Moeed
>>
>> ========================================
>> step 164300, remaining runtime: 241 s step 164400, remaining
>> runtime: 240 s step 164500, remaining runtime: 240 s
>> step 164600, remaining runtime: 239 s Warning: 1-4 interaction
>> between 260 and 267 at distance 73679654.990 which is larger than the 1-4
>> table size 2.250 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
>> =========================================
>> results till t=320 ps (before first run crash)
>> fourierspacing = 0.12
>>
>> LJ-14 757.246 26.6239 26.5661 -0.0189929
>> -6.07777
>>
>> Coulomb-14 -186.509 15.9866 15.9529 -0.0112174
>> -3.5896
>>
>> LJ (SR) -2691.84 117.026 107.231 -0.507373
>> -162.361
>>
>> Coulomb (SR) 725.662 17.6483 17.5876 0.0158275
>> 5.06483
>>
>>
>> fourierspacing = 0.3
>>
>>
>> LJ-14 757.129 26.4936 26.4578 -0.0149128
>> -4.77214
>>
>> Coulomb-14 -199.523 14.949 14.158 -0.0519427
>> -16.6218
>>
>> LJ (SR) -2670.5 111.201 109.688 0.19784
>> 63.3092
>>
>> Coulomb (SR) 739.794 16.1807 15.4473 0.0521352
>> 16.6834
>>
>> ====================================================
>> pbc = xyz
>> ; Run control integrator = md
>> dt = 0.002 nsteps
>> = 1000000 ;5000 nstcomm = 100
>> ; Output control
>> nstenergy = 100 nstxout = 100
>> nstvout = 0
>> nstfout = 0
>> nstlog = 1000 nstxtcout = 1000
>>
>> ; Neighbor searching
>> nstlist = 10 ns_type = grid
>>
>> ; Electrostatics/VdW
>> coulombtype = PME vdw-type = Shift
>> rcoulomb-switch = 0 rvdw-switch =
>> 0.9 ;0
>> ; Cut-offs
>> rlist = 1.25 rcoulomb = 1.25
>> ;1.1 rvdw = 1.0
>> ; PME parameters
>> fourierspacing = 0.3 fourier_nx = 0
>> fourier_ny = 0
>> fourier_nz = 0
>> pme_order = 4 ewald_rtol = 1e-5
>> optimize_fft = yes
>>
>> ; Temperature coupling Tcoupl = v-rescale
>> tc-grps = System ;HEX tau_t =
>> 0.1 ;0.1 ref_t = 400 ;300
>>
>> ; Pressure coupling
>> Pcoupl = Parrinello-Rahman Pcoupltype =
>> isotropic tau_p = 1 1 ;0.5
>> compressibility = 4.5e-5 4.5e-5 ref_p =
>> 70 70
>> ; Velocity generation gen_vel = yes
>> gen_temp = 300.0 gen_seed =
>> 173529
>> ; Bonds
>> constraints = all-bonds constraint-algorithm =
>> lincs
>>
>>
> --
> ========================================
>
> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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--
Moeed Shahamat
Graduate Student (Materials Modeling Research Group)
McGill University- Department of Chemical Engineering
Montreal, Quebec H3A 2B2, Canada
Web:
http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php
Web:http://mmrg.chemeng.mcgill.ca/
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