Hi, All,<div> I'm trying to see if anybody has experience of using the interface of gromacs and ORCA(since it's free). I know that the following link gave information on how</div><div><a href="http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code">http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code</a></div>
<div> But.....But, the gromacs in the above link is quite old(3.2). I download the latest 4.5.3 and followed the instructions in the above link and I was trying to optimize an simple cluster(no pbc) where part of it are treated using QM. here is the example mdp file</div>
<div>=========================================================================================================================</div><div><div>title = cpeptide</div><div>integrator = steep ;integrator includes energy minimization algorithms</div>
<div>dt = 0.002 ; ps !</div><div>nsteps = 10000</div><div>nstlist = 1</div><div>ns_type = simple</div><div>rlist = 3.0</div><div>rcoulomb = 3.0</div>
<div>coulombtype = cut-off</div><div>vdwtype = cut-off</div><div>rvdw = 3.0</div><div>pbc = no</div><div>periodic_molecules = no</div><div>constraints = none</div>
<div>energygrps = qm_part mm_part</div><div>; QM/MM calculation stuff</div><div>QMMM = yes</div><div>QMMM-grps = qm_part</div><div>QMmethod = rhf</div><div>QMbasis = 3-21G</div><div>QMMMscheme = oniom</div><div>QMcharge = 0</div>
<div>QMmult = 1</div><div>;</div><div>; Energy minimizing stuff</div><div>;</div><div>emtol = 60 ; minimization thresold (kj/mol.nm-1) 1 hartree/bohr= 49614.75241 kj/mol.nm-1 1 kj/mol.nm-1=2.01553e-5 hartree/bohr</div>
<div>emstep = 0.01 ; minimization step in nm</div><div>=========================================================================================================================</div></div><div>I set up the BASENAME and ORCA_PATH as told in the instruction.</div>
<div>first of all, the normal electronic embedding just simply gave segmentation fault error right after the it prints information on number of steps of optimization.</div><div><br></div><div>So I switch to ONIOM, this time, at least, orca is called and energy and gradient are both generated. However, when it comes to read the energy and gradient, it always crashes when tried to read gradient, this is at <b>line 346</b> source code src/mdlib/qm_orca.c</div>
<div>============================================</div><div>sscanf(buf,"%lf\n", &QMgrad[k][XX]);</div><div>============================================</div><div>a segmentation fault error is printed. If I replace the &QMgrad[k][XX] by an temporary variable temp </div>
<div> sscanf(buf,"%lf\n", &temp);</div><div>temp gets the correct value and if I use,</div><div>QMgrad[k][XX]=temp </div><div>and tries to print QMgrad[k][XX], a bus error will be printed.</div><div>I did some research online, seems that usually this implies an memory bug in the code which is the most difficult bug one can ever encounter.</div>
<div>So has anyone successfully used gromacs and orca to do QMMM?</div><div>Generally, would anyone recommend using gromacs to do QMMM?</div><div><br></div><div>Cheers,</div><div>Xiaohu</div>