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