Hi, <br>When I do the DNA MD simulation. I use pdb2gmx, and the water model I used is spc.gro. <br>I did the editconf and genbox. The following is my em.mdp file. <br>------------------------------------------------------------------------------------------------
<br>define =-DEFLEXIBLE <br>integrator = steep<br>;gen-vel = yes<br>;pbc = no<br>;comm_mode = angular<br>nsteps = 2000<br>epsilon_rf = 82<br>nstlist = 100
<br>ns_type = grid<br>rlist = 1.3<br>dt = 0.0005<br>tc-grps = system<br>tcoupl = Berendsen<br>;freezegrps = CNT<br>;freezedim = N<br>tau-t = 0.1<br>temp = 450
<br>ref-t = 450<br>;pcoupl = Parrinello-Rahman<br>;pcoupltype = isotropic<br>;tau-p = 0.5<br>;ref_p = 1.01325<br>;compressibility = 4.5e-5<br>coulombtype = pme<br>rcoulomb =
1.3<br>vdw-type = cut-off<br>rvdw = 1.3<br>nstenergy = 10<br>optimize_fft = yes<br>emstep = 0.2<br>emtol = 100<br>constraints = none<br>-------------------------------------------------------------------------------------
<br>Q1, I am not sure whether should I put the "define = -DFLEXIBLE" in the em.mdp.<br>Q2,<br>When I perform the preprocess for energy minimization (grompp), the error message is :<br>"Fatal error:<br>[file "/home/nano/gromacs/share/gromacs/top/spc.itp", line 41]:
<br> Atom index(1) in setttles out of bounds (1-0)"<br><br>I looked back to the spc.itp, from line 39 to 41:<br>----------------------------------------------------------------------<br>[ settles ]<br>; OW funct doh dhh
<br>1 1 0.1 0.16330<br>---------------------------------------------------------------------<br>Can you give me any suggestions about how to correct it and why?<br><br>Best regards!<br>Bo<br>