Dear all,<br> I am trying to minimize a protein structure but i noticed initially before it starts minimization, it gives warning<br>-------------------------------------<br>Warning: 1-4 interaction between 1434 and 1490 at distance 1.783 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>Using 10 BFGS correction steps.<br><br> F-max = 7.89523e+03 on atom 1185<br>
F-Norm = 4.87025e+04<br> ------------------------------<br>finally it converged to machine precision but not to the requested precision Fmax < 1000. When i view final structure, it<br>looks the residues are sprayed out. The mdp file which i used for minimization is <br>
------------------------------------------------------------------------------------<br>Title = protien test<br>cpp = /lib/cpp<br>;include = -I../top<br>define = -DFLEXIBLE<br>
constraints = none<br>integrator = steep<br>nstcomm = 1<br>dt = 0.002 ; ps !<br>nsteps = 50000<br>nstlist = 10<br>ns_type = grid<br>
rlist = 1.4<br>coulombtype = shift<br>rcoulomb = 1.2<br>vdwtype = shift<br>rvdw = 1.2<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 1000.0<br>
emstep = 0.01<br><br>------------------------------------------------------------<br><br><br>This protein structure has been minimized using Charmm but in gromacs i am having problem. Can anyone help me. Thank you.<br>
Rama<br><br><br>