<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Dear all,</DIV>
<DIV> </DIV>
<DIV>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".</DIV>
<DIV> </DIV>
<DIV>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.</DIV>
<DIV> </DIV>
<DIV>I attached the last steps of log file and used mdp file.</DIV>
<DIV> </DIV>
<DIV>Thank you very much in advance for solution suggestions.</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Serdar Durdagi</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>
<DIV>title = CB1_conf_a MD</DIV>
<DIV>cpp = /usr/bin/cpp</DIV>
<DIV>constraints = all-bonds</DIV>
<DIV>integrator = md</DIV>
<DIV>dt = 0.002 ; ps !</DIV>
<DIV>nsteps = 1250000 </DIV>
<DIV>nstcomm = 1</DIV>
<DIV>nstxout = 500 </DIV>
<DIV>nstvout = 0</DIV>
<DIV>nstfout = 0</DIV>
<DIV>nstlog = 500</DIV>
<DIV>nstlist = 10</DIV>
<DIV>ns_type = grid</DIV>
<DIV>rlist = 1.0</DIV>
<DIV>coulombtype = PME</DIV>
<DIV>rcoulomb = 1.0</DIV>
<DIV>vdwtype = cut-off</DIV>
<DIV>rvdw = 1.4</DIV>
<DIV>fourierspacing = 0.12</DIV>
<DIV>fourier_nx = 0</DIV>
<DIV>fourier_ny = 0</DIV>
<DIV>fourier_nz = 0</DIV>
<DIV>pme_order = 4</DIV>
<DIV>ewald_rtol = 1e-5</DIV>
<DIV>optimize_fft = yes</DIV>
<DIV>; Berendsen temperature coupling is on</DIV>
<DIV>Tcoupl = berendsen</DIV>
<DIV>tau_t = 0.1 0.1 0.1 </DIV>
<DIV>tc-grps = DPP C6 SOL</DIV>
<DIV>ref_t = 300 300 300</DIV>
<DIV>; Pressure coupling is on</DIV>
<DIV>Pcoupl = no</DIV>
<DIV>tau_p = 0.5</DIV>
<DIV>compressibility = 4.5e-5</DIV>
<DIV>ref_p = 1.0</DIV>
<DIV>Generate velocities is on at 300 K.</DIV>
<DIV>gen_vel = yes</DIV>
<DIV>gen_temp = 300.0</DIV>
<DIV>gen_seed = 173529</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> Step Time Lambda<BR> 166500 333.00000 0.00000</DIV>
<DIV> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.006301 4163 4164 0.001222<BR> After LINCS 0.000144 27 28 0.000006</DIV>
<DIV> Energies (kJ/mol)<BR> Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14<BR> 1.08817e+04 2.92391e+03 5.33679e+03 3.48481e+02 1.18752e+03<BR> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.<BR> 1.33953e+04 -6.78212e+03 -2.28400e+03 -1.91715e+05 -1.13117e+05<BR> Potential Kinetic En. Total Energy Temperature Pressure (bar)<BR> -2.79825e+05 4.07337e+04 -2.39091e+05
3.03482e+02 -3.62649e+02</DIV>
<DIV> Step Time Lambda<BR> 167000 334.00000 0.00000</DIV>
<DIV> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.006221 2094 2095 0.001243<BR> After LINCS 0.000050 27 28 0.000004</DIV>
<DIV> Energies (kJ/mol)<BR> Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14<BR> 1.11706e+04 2.98252e+03 5.26699e+03 3.75113e+02 1.34753e+03<BR> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.<BR> 1.30631e+04 -7.42424e+03 -2.27672e+03 -1.89582e+05 -1.12967e+05<BR> Potential Kinetic En. Total Energy Temperature Pressure (bar)<BR> -2.78044e+05 3.95852e+04 -2.38459e+05
2.94925e+02 -2.05298e+02</DIV>
<DIV> Step Time Lambda<BR> 167500 335.00000 0.00000</DIV>
<DIV> Rel. Constraint Deviation: Max between atoms RMS<BR> Before LINCS 0.005474 693 694 0.001211<BR> After LINCS 0.000078 27 28 0.000004</DIV>
<DIV> Energies (kJ/mol)<BR> Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14<BR> 1.10570e+04 2.92074e+03 5.41756e+03 3.52792e+02 1.27318e+03<BR> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.<BR> 1.29374e+04 -7.77397e+03 -2.27790e+03 -1.89057e+05 -1.13016e+05<BR> Potential Kinetic En. Total Energy Temperature Pressure (bar)<BR> -2.78166e+05 4.01726e+04 -2.37993e+05
2.99302e+02 -2.13536e+02</DIV>
<DIV><BR>Step 167969, time 335.938 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max inf (between atoms 3 and 4) rms inf<BR>bonds that rotated more than 30 degrees:<BR> atom 1 atom 2 angle previous, current, constraint length<BR> 2 3 31.7 0.1530 0.1802 0.1530<BR> 3 4 71.9 0.1530 2265021108479420332760918618026182082596758987575428182455396865361974544095646526528815104.0000 0.1530<BR> 4 5 84.9 0.1530 18122984199645729100337329541298157025024538645594811987064424745522897956771954290799411200.0000 0.1530<BR>
5 6 86.3 0.1530 119175309066877201840333474141339178556441000114517345446131726568065607288857704216068620288.0000 0.1530<BR> 6 7 83.2 0.1530 319516206321530845988576783668094567874060447793487769269077323346592450103529992297220407296.0000 0.1530<BR> 7 8 90.1 0.1852 1215659572675149285233162397268999839681310750651580520597516723093456091315807918022002212864.0000 0.1852<BR> 7 11 90.0 0.3827 261046278995437240163010555897466446819104052294790175823713013006178876940639100930185232384.0000
0.3827<BR> 7 12 85.9 2.1222 708122676010602206123407194621458163923965667621590605923744064304768598320784768943452585984.0000 2.1222<BR> 8 9 89.7 0.1830 1464090871981283196025364104977632977506718699519384307354293090385664459392658757834091003904.0000 0.1830<BR> 9 10 89.4 0.1530 1642496700465256611058147631762101542391865462505379007077289495407248437142902530819236036608.0000 0.1530<BR> 10 11 90.1 0.1830 756767949452499811070392082343079516984060143555343448612396645526001354011557126580748681216.0000
0.1830<BR> 12 13 93.3 0.1390 1675013654744810844287719234237265294947410972536560437889789182123995586451476744156309618688.0000 0.1390<BR> 12 14 85.1 0.1390 329283409277106964914359855618901648092274440312854462821854172823229415900192821585052172288.0000 0.1390<BR> 13 28 92.0 0.1390 704336240987254356289474657410431622881423034652003910924693084338836951238889120976668196864.0000 0.1390<BR> 14 15 99.1 0.1390 379860931583656159501355512782081590450061932169874874128503353575000723021905332351770034176.0000
0.1390<BR> 15 16 90.1 1.4429 206242205098337185268222500120712681530171088335436475613630821288724906666004435554722119680.0000 1.4429<BR> 15 27 91.8 0.1390 398684384369289490166841022015490990129049715188945258148097433284725455687338625841045176320.0000 0.1390<BR> 16 17 124.5 0.1435 5471440768467994537804435788744902781374726537963888385752468854524825194082290680987648000.0000 0.1435<BR> 17 18 78.2 0.1530 1217841628171641512793797538386485535450621055372659463190106114383330186479756409921601536.0000
0.1530<BR> 17 19 80.7 0.1530 1217841628171641512793797538386485535450621055372659463190106114383330186479756409921601536.0000 0.1530<BR> 17 20 113.4 0.1530 4056018304815038460726471748512358923224231361828694303945468971580026881584083840777846784.0000 0.1530<BR> 20 21 104.5 0.1530 5069114535236862410529809697539370521064020867182026484700468134800923155949405760991002624.00</DIV>
<DIV> </DIV>
<DIV> </DIV></DIV>
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