[gmx-users] LINCS warning
serdar durdagi
durdagis at yahoo.de
Thu Aug 14 17:48:15 CEST 2008
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.
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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