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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