Sheyore Omovie wrote:
Thanks Tom,
I have tried that in the past though, and I still get Epot values of nan.
One solution is to take your (successful) individual .top files and edit
them in line with the example in chapter 5 to create .itp files for your
two molecules. Then include them both in a master .top, set up a
structure file with both molecules and use editconf and genbox and
grompp in the usual way.
It seems the only other option I have is to place the molecules in
separate boxes, set
disre=simple, and use the -multi option during the mdrun. The -multi
option only works with the parallel installation.
-multi allows you to do multiple independent simulations. This won't do
anything differently for you than doing the independent simulations
asynchronously.
Unfortunately I get the ff error message when I try to use the parallel
gromacs installation on the server:
/<MPICH-MX> Error: Need to obtain the job magic number in MXMPI_MAGIC./
/I would appreciate any advice on how to fix this./
This is an MPI problem, not a GROMACS problem. Consult your sysadmins.
Mark
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