Hello Mark, thanks for your attention. <br> I had already made some
attempts setting the two molecules <br>in the same block (as suggested in
the forum) but I had no success. <br>I tried to
use restraints and constraints and but run always fails. <br><br>Please I am sending my .mdp and .top files as well as the error <br>message that I getting. Note, there is no bonded parameters molecules<br>between two molecules.<br>
<br> Can you help me to solve this problem?<br><br><br>>>>>> .mdp file<br>cpp =<br>integrator = md<br>tinit = 0.0<br>dt = 0.01<br>nsteps = 10000<br>
nstcomm = 1<br>nstxout = 1000<br>nstvout = 0<br>nstfout = 0<br>nstlog = 1000<br>nstenergy = 1000<br>nstxtcout = 1000 # with 1000 we get 10000/1000 == 10 (+ original, t=0) frames<br>
xtc_precision = 1000<br>nstlist = 10<br>energygrps =<br>ns_type = grid<br>rlist = 0.9<br>coulombtype = cut-off<br>rcoulomb = 0.9<br>rvdw = 0.9<br>
Tcoupl = Berendsen<br>tc_grps = system<br>ref_t = 90<br>tau_t = 0.2<br>Pcoupl = No<br>tau_p = 1.0<br>compressibility = 1e-4<br>ref_p = 1.0<br>
gen_vel = yes<br>gen_temp = 90<br>gen_seed = 173529<br>free-energy = yes<br>init-lambda = 0.96<br>delta-lambda = -.000064 # in order to get down to .32 nm with 10000 steps<br><br>>>>><br>
#include "ffoplsaa.itp"<br><br>[ moleculetype ]<br>; Name nrexcl<br>BEN 3<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br>
1 opls_075 1 BEN C1 1 0 13.019 ; qtot 0<br> 2 opls_075 1 BEN C2 2 0 13.019 ; qtot 0<br> 3 opls_075 1 BEN C3 3 0 13.019 ; qtot 0<br>
4 opls_075 1 BEN C4 4 0 13.019 ; qtot 0<br> 5 opls_075 1 BEN C5 5 0 13.019 ; qtot 0<br> 6 opls_075 1 BEN C6 6 0 13.019 ; qtot 0<br>
7 opls_075 2 BEN C1 7 0 13.019 ; qtot 0<br> 8 opls_075 2 BEN C2 8 0 13.019 ; qtot 0<br> 9 opls_075 2 BEN C3 9 0 13.019 ; qtot 0<br>
10 opls_075 2 BEN C4 10 0 13.019 ; qtot 0<br> 11 opls_075 2 BEN C5 11 0 13.019 ; qtot 0<br> 12 opls_075 2 BEN C6 12 0 13.019 ; qtot 0<br>
<br>[ bonds ]<br>; ai aj funct c0 c1 c2 c3<br> 1 2 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05<br> 1 6 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05<br>
2 3 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05<br> 3 4 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05<br> 4 5 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05<br>
5 6 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05<br> 7 8 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05<br> 7 12 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05<br>
8 9 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05<br> 9 10 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05<br> 10 11 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05<br>
11 12 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05<br><br>[ pairs ]<br>; ai aj funct c0 c1 c2 c3<br> 1 4 1<br> 2 5 1<br> 3 6 1<br>
7 10 1<br> 8 11 1<br> 9 12 1<br><br>[ angles ]<br>; ai aj ak funct c0 c1 c2 c3<br> 2 1 6 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02<br>
1 2 3 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02<br> 2 3 4 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02<br> 3 4 5 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02<br>
4 5 6 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02<br> 1 6 5 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02<br> 8 7 12 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02<br>
7 8 9 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02<br> 8 9 10 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02<br> 9 10 11 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02<br>
10 11 12 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02<br> 7 12 11 1 1.200000e+02 4.000000e+02 1.200000e+02 4.000000e+02<br><br>[ dihedrals ]<br>; ai aj ak al funct c0 c1 c2 c3 c4 c5<br>
6 1 2 3 3 1.800000e+02 5.000000e+00 3.000000e+00 1.800000e+02 5.000000e+00 3.000000e+00<br> 2 1 6 5 3 1.800000e+02 5.000000e+00 3.000000e+00 1.800000e+02 5.000000e+00 3.000000e+00<br>
1 2 3 4 3 1.800000e+02 5.000000e+00 3.000000e+00 1.800000e+02 5.000000e+00 3.000000e+00<br> 2 3 4 5 3 1.800000e+02 5.000000e+00 3.000000e+00 1.800000e+02 5.000000e+00 3.000000e+00<br>
3 4 5 6 3 1.800000e+02 5.000000e+00 3.000000e+00 1.800000e+02 5.000000e+00 3.000000e+00<br> 4 5 6 1 3 1.800000e+02 5.000000e+00 3.000000e+00 1.800000e+02 5.000000e+00 3.000000e+00<br>
12 7 8 9 3 1.800000e+02 5.000000e+00 3.000000e+00 1.800000e+02 5.000000e+00 3.000000e+00<br> 8 7 12 11 3 1.800000e+02 5.000000e+00 3.000000e+00 1.800000e+02 5.000000e+00 3.000000e+00<br>
7 8 9 10 3 1.800000e+02 5.000000e+00 3.000000e+00 1.800000e+02 5.000000e+00 3.000000e+00<br> 8 9 10 11 3 1.800000e+02 5.000000e+00 3.000000e+00 1.800000e+02 5.000000e+00 3.000000e+00<br>
9 10 11 12 3 1.800000e+02 5.000000e+00 3.000000e+00 1.800000e+02 5.000000e+00 3.000000e+00<br> 10 11 12 7 3 1.800000e+02 5.000000e+00 3.000000e+00 1.800000e+02 5.000000e+00 3.000000e+00<br>
<br>[ position_restraints ]<br>; atom type fx fy fz<br> 1 1 1000 1000 1000<br> 7 1 1000 1000 1000<br><br>;[ constraints ]<br>; ai aj ft A B<br>; 1 7 2 0.0 1.0<br>
<br>[ system ]<br>; Name<br>BEN<br><br>[ molecules ]<br>; Compound #mols<br>BEN 1<br><br><br>>>> Error mensage<br><br><br>Back Off! I just backed up dgdl.xvg to ./#dgdl.xvg.2#<br>starting mdrun 'BEN'<br>
10000 steps, 100.0 ps.<br><br><br>Back Off! I just backed up traj.trr to ./#traj.trr.3#<br><br>Back Off! I just backed up traj.xtc to ./#traj.xtc.2#<br>Warning: 1-4 interaction between 1 and 4 at distance 419.707 which is larger than the 1-4 table size 1.000 nm<br>
These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br clear="all">_______________________________________<br>Eudes Eterno Fileti<br>
Centro de Ciências Naturais e Humanas<br>Universidade Federal do ABC<br>Rua Santa Adélia, 166 - Bloco B, Sala 1048<br>09210-170 Santo André - SP Brasil<br>+55.11.4437-8408<br>skype: eefileti<br><a href="http://cromo.ufabc.edu.br/%7Efileti/" target="_blank">http://cromo.ufabc.edu.br/~fileti/</a><br>