[gmx-users] LINCS warning
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 14 17:58:32 CEST 2008
serdar durdagi wrote:
> Dear all,
>
> I am making "drg+lipid" simulations with gmx. From the 9 series of
> experiments all of them worked fine for 250 ps equilubration run.
> However, when I start the real simulation, 4 of them stopped after 300
> ps (I have setted the simualtion time to 2.5 ns). It complains the LINCS
> warning. "relative constraint deviation after LINC".
>
> All the systems are very similar, just different conformations of drug.
> So, I can not see any reason why some of them are working fine and some
> of them not.
>
Those different conformations may have different (bad) interactions with the
other elements of your system. Having described nothing about your preparation,
minimization, or equilibration scheme, that's about the best I can see to offer.
View the trajectory and see where things are starting to explode. That will
give you a hint as to where the problem lies. There are hundreds of posts about
LINCS warnings in the mailing list archive, as well as the following wiki site:
http://wiki.gromacs.org/index.php/blowing_up
These sources should provide you with many things to try.
One final note: Depending on the size of these drug molecules, it may not be
appropriate to couple them to their own temperature bath. Insufficient degrees
of freedom (i.e., coupling a few ions to their own bath) can lead to the same
type of weird, random explosions. For more information, again, consult the wiki:
http://wiki.gromacs.org/index.php/Thermostats
-Justin
> I attached the last steps of log file and used mdp file.
>
> Thank you very much in advance for solution suggestions.
>
>
> Serdar Durdagi
>
>
> title = CB1_conf_a MD
> cpp = /usr/bin/cpp
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 1250000
> nstcomm = 1
> nstxout = 500
> nstvout = 0
> nstfout = 0
> nstlog = 500
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> vdwtype = cut-off
> rvdw = 1.4
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on
> Tcoupl = berendsen
> tau_t = 0.1 0.1 0.1
> tc-grps = DPP C6 SOL
> ref_t = 300 300 300
> ; Pressure coupling is on
> Pcoupl = no
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> Generate velocities is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
>
>
>
>
> Step Time Lambda
> 166500 333.00000 0.00000
> Rel. Constraint Deviation: Max between atoms RMS
> Before LINCS 0.006301 4163 4164 0.001222
> After LINCS 0.000144 27 28 0.000006
> Energies (kJ/mol)
> Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
> 1.08817e+04 2.92391e+03 5.33679e+03 3.48481e+02 1.18752e+03
> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.
> 1.33953e+04 -6.78212e+03 -2.28400e+03 -1.91715e+05 -1.13117e+05
> Potential Kinetic En. Total Energy Temperature Pressure (bar)
> -2.79825e+05 4.07337e+04 -2.39091e+05 3.03482e+02 -3.62649e+02
> Step Time Lambda
> 167000 334.00000 0.00000
> Rel. Constraint Deviation: Max between atoms RMS
> Before LINCS 0.006221 2094 2095 0.001243
> After LINCS 0.000050 27 28 0.000004
> Energies (kJ/mol)
> Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
> 1.11706e+04 2.98252e+03 5.26699e+03 3.75113e+02 1.34753e+03
> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.
> 1.30631e+04 -7.42424e+03 -2.27672e+03 -1.89582e+05 -1.12967e+05
> Potential Kinetic En. Total Energy Temperature Pressure (bar)
> -2.78044e+05 3.95852e+04 -2.38459e+05 2.94925e+02 -2.05298e+02
> Step Time Lambda
> 167500 335.00000 0.00000
> Rel. Constraint Deviation: Max between atoms RMS
> Before LINCS 0.005474 693 694 0.001211
> After LINCS 0.000078 27 28 0.000004
> Energies (kJ/mol)
> Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
> 1.10570e+04 2.92074e+03 5.41756e+03 3.52792e+02 1.27318e+03
> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.
> 1.29374e+04 -7.77397e+03 -2.27790e+03 -1.89057e+05 -1.13016e+05
> Potential Kinetic En. Total Energy Temperature Pressure (bar)
> -2.78166e+05 4.01726e+04 -2.37993e+05 2.99302e+02 -2.13536e+02
>
> Step 167969, time 335.938 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max inf (between atoms 3 and 4) rms inf
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 2 3 31.7 0.1530 0.1802 0.1530
> 3 4 71.9 0.1530
> 2265021108479420332760918618026182082596758987575428182455396865361974544095646526528815104.0000
> 0.1530
> 4 5 84.9 0.1530
> 18122984199645729100337329541298157025024538645594811987064424745522897956771954290799411200.0000
> 0.1530
> 5 6 86.3 0.1530
> 119175309066877201840333474141339178556441000114517345446131726568065607288857704216068620288.0000
> 0.1530
> 6 7 83.2 0.1530
> 319516206321530845988576783668094567874060447793487769269077323346592450103529992297220407296.0000
> 0.1530
> 7 8 90.1 0.1852
> 1215659572675149285233162397268999839681310750651580520597516723093456091315807918022002212864.0000
> 0.1852
> 7 11 90.0 0.3827
> 261046278995437240163010555897466446819104052294790175823713013006178876940639100930185232384.0000
> 0.3827
> 7 12 85.9 2.1222
> 708122676010602206123407194621458163923965667621590605923744064304768598320784768943452585984.0000
> 2.1222
> 8 9 89.7 0.1830
> 1464090871981283196025364104977632977506718699519384307354293090385664459392658757834091003904.0000
> 0.1830
> 9 10 89.4 0.1530
> 1642496700465256611058147631762101542391865462505379007077289495407248437142902530819236036608.0000
> 0.1530
> 10 11 90.1 0.1830
> 756767949452499811070392082343079516984060143555343448612396645526001354011557126580748681216.0000
> 0.1830
> 12 13 93.3 0.1390
> 1675013654744810844287719234237265294947410972536560437889789182123995586451476744156309618688.0000
> 0.1390
> 12 14 85.1 0.1390
> 329283409277106964914359855618901648092274440312854462821854172823229415900192821585052172288.0000
> 0.1390
> 13 28 92.0 0.1390
> 704336240987254356289474657410431622881423034652003910924693084338836951238889120976668196864.0000
> 0.1390
> 14 15 99.1 0.1390
> 379860931583656159501355512782081590450061932169874874128503353575000723021905332351770034176.0000
> 0.1390
> 15 16 90.1 1.4429
> 206242205098337185268222500120712681530171088335436475613630821288724906666004435554722119680.0000
> 1.4429
> 15 27 91.8 0.1390
> 398684384369289490166841022015490990129049715188945258148097433284725455687338625841045176320.0000
> 0.1390
> 16 17 124.5 0.1435
> 5471440768467994537804435788744902781374726537963888385752468854524825194082290680987648000.0000
> 0.1435
> 17 18 78.2 0.1530
> 1217841628171641512793797538386485535450621055372659463190106114383330186479756409921601536.0000
> 0.1530
> 17 19 80.7 0.1530
> 1217841628171641512793797538386485535450621055372659463190106114383330186479756409921601536.0000
> 0.1530
> 17 20 113.4 0.1530
> 4056018304815038460726471748512358923224231361828694303945468971580026881584083840777846784.0000
> 0.1530
> 20 21 104.5 0.1530
> 5069114535236862410529809697539370521064020867182026484700468134800923155949405760991002624.00
>
>
>
>
>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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