<table cellspacing='0' cellpadding='0' border='0' ><tr><td style='font: inherit;'><P>Dear users,</P>
<P>I have a problem on running MD of 146 LC molecules system. I do not do the energy minimisation. I use NVT ensemble to equilibrate my system. My topology was created using PRODRG beta server. After the creation of my systems box (on top of each other)</P>
<P> </P>
<P>1. editconf -f lc -bt d -box 1.3 0.02 0.02 -princ -c -d 0.5 -rvdw 0.12 -o lcc</P>
<P>2. genconf -f lcc -nbox 8 8 8 -dist 0 0 0 -nmolat 27 -o lc512</P>
<P> </P>
<P>I put inside another (a little bigger) molecule</P>
<P> </P>
<P>3. editconf -f sl -bt c -box 6 -princ -c -d 2.5 -rvdw 0.12 -o sll</P>
<P>4. genbox -cp sll -cs lc512 -o slw -p sl</P>
<P> </P>
<P>then create tpr</P>
<P> </P>
<P>5. grompp -v -np 32 -shuffle -sort -f eq.mdp -c slw -p sl -o topol.tpr</P>
<P>and submit the job</P>
<P> </P>
<P>I always get my system exploding</P>
<P> </P><FONT size=1>
<P>Initializing LINear Constraint Solver</P>
<P>number of constraints is 122</P>
<P>average number of constraints coupled to one constraint is 3.0</P>
<P>Rel. Constraint Deviation: Max between atoms RMS</P>
<P>Before LINCS 0.086035 40 39 0.026421</P>
<P>After LINCS 0.000704 103 104 0.000292</P>
<P>Energies (kJ/mol)</P>
<P>G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14</P>
<P>2.76783e+03 8.11377e+01 8.21662e+01 3.98602e+04 5.57164e+03</P>
<P>LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Potential</P>
<P>2.71048e+03 -1.88575e+02 -3.38992e+03 -3.62073e+04 1.12877e+04</P>
<P>Kinetic En. Total Energy Temperature Pressure (bar)</P>
<P>6.65517e+04 7.78394e+04 2.06669e+03 1.75872e+05</P>
<P> </P>
<P>Step 86, time 0.172 (ps) LINCS WARNING</P>
<P>relative constraint deviation after LINCS:</P>
<P>max 96.909290 (between atoms 85 and 86) rms 10.933811</P>
<P>bonds that rotated more than 30 degrees:</P>
<P>atom 1 atom 2 angle previous, current, constraint length</P>
<P>77 78 113.7 0.1390 0.5917 0.1390</P>
<P>77 87 116.3 0.1390 0.5570 0.1390</P>
<P>78 79 109.8 0.1090 0.5917 0.1090</P>
<P>78 80 104.4 0.1390 1.2899 0.1390</P>
<P>80 81 93.6 0.1090 5.0458 0.1090</P>
<P>82 80 99.8 0.1390 3.9224 0.1390</P>
<P>82 83 100.5 0.1430 3.8921 0.1430</P>
<P>82 85 99.9 0.1390 3.9638 0.1390</P>
<P>83 84 103.4 0.1140 3.1119 0.1140</P>
<P>85 86 91.7 0.1090 10.6721 0.1090</P>
<P>85 87 100.2 0.1390 1.7797 0.1390</P>
<P>87 88 110.3 0.1090 0.5717 0.1090</P>
<P>Constraint error in algorithm Lincs at step 86</P>
<P>Wrote pdb files with previous and current coordinates</P>
<P>Large VCM(group rest): -949890684120872786061526585043023133196136319944012857455888493019588547485855908650717825011817737590092000256377384500897124503083675335640562545921274578670325230339034153228858928503740516247758241500986457604229169152.00000, -7700177673405372508341068198495354437944151718908865834595177256517607987036524874348348597888871194101005699859793685064099787214560958505758284878533509661264882479706501126070295847653568962516830194295490734095350104064.00000, -17482030675841594076114066100363479435124387445824631353703195421406478322250794440904806833364056039859394683424411714469447896344546474426178109668279235955517800609185251692588873229116161214420413237478774727134943379456.00000, ekin-cm: inf</P>
<P> </P>
<P><STRONG>MDP file</STRONG></P>
<P> </P><FONT size=1>
<P>title = molecular dynamics</P>
<P>cpp = /usr/bin/cpp</P>
<P>include = -I../top</P>
<P>; RUN CONTROL PARAMETERS</P>
<P>integrator = md</P>
<P>dt = 0.002 ;ps</P>
<P>nsteps = 5000000 ;10 ns</P>
<P>;comm_mode = Angular ;remove center of mass translation and rotation around the center of mass</P>
<P>nstcomm = 1 ;number of steps for center of mass motion removal</P>
<P>; OUTPUT CONTROL OPTIONS</P>
<P>nstxout = 100 ;every 0.2 ps</P>
<P>nstvout = 100</P>
<P>nstfout = 0</P>
<P>nstlog = 100 ;Output frequency to write energies to log file </P>
<P>nstenergy = 100 ;Output frequency to write energies to energy file </P>
<P>energygrps = MMM DRG ;Selection of energy groups</P>
<P>; NEIGHBOR SEARCHING PARAMETERS</P>
<P>nstlist = 1 ;update frequency </P>
<P>ns_type = grid ;algorithm (simple or grid)</P>
<P>pbc = xyz</P>
<P>rlist = 1.2 ;cut-off distance nm </P>
<P>; OPTIONS FOR ELECTROSTATICS</P>
<P>coulombtype = PME ;Method for doing electrostatics </P>
<P>rcoulomb = 1.2 ;Coulomb cut-off distance nm </P>
<P>epsilon-r = 1.0 ;relative dielectric constant</P>
<P>; VDW</P>
<P>vdw-type = Cut-off ;Method for doing VDW</P>
<P>rvdw = 1.5 ;cut-off lengths nm</P>
<P>;DispCorr = EnerPres ;Apply long range dispersion corrections for Energy and Pressure</P>
<P>fourierspacing = 0.1 ;Spacing for the PME/PPPM FFT grid</P>
<P>; EWALD/PME/PPPM parameters</P>
<P>pme_order = 4 ;cubic interpolation</P>
<P>ewald_rtol = 1e-05 ;relative Evald-shifted potential at cut-off</P>
<P>optimize_fft = yes ;calculate at startup</P>
<P>; OPTIONS FOR WEAK COUPLING ALGORITHMS</P>
<P>Tcoupl = Berendsen ;Temperature coupling </P>
<P>Tc-grps = System ;Groups to couple separately</P>
<P>tau_T = 5.0 ;Time constant (ps)</P>
<P>ref_T = 299 ;reference temperature (K)</P>
<P>Pcoupl = no ;Pressure coupling</P>
<P>Pcoupltype = Isotropic</P>
<P>tau_P = 5.0 ;Time constant (ps)</P>
<P>compressibility = 4.5e-5 ;compressibility (1/bar)</P>
<P>ref_P = 1.0 ;reference P (bar)</P>
<P>; OPTIONS FOR BONDS </P>
<P>constraints = all-bonds</P>
<P>constraint-algorithm = lincs</P>
<P>;shake_tol = 0.0001</P>
<P>unconstrained-start = yes ;don't constrain the start configuration</P>
<P>lincs-order = 4 ;Highest order in the expansion of the constraint coupling matrix</P>
<P>lincs-warnangle = 30</P>
<P>lincs-iter = 2</P>
<P>morse = no ;Convert harmonic bonds to morse potentials</P>
<P>;GENERATE VELOCITES</P>
<P>gen_vel = no ;generates velocities</P>
<P>gen_temp = 299 </P>
<P>gen_seed = 173529</P></FONT>
<P> </P>
<P>Could anyone help me?</P>
<P> </P>
<P>Thanks</P>
<P> </P>
<P>Egidijus Kuprusevicius</P></FONT></td></tr></table><br>
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