Mathieu, Jennifer J. wrote:
I've searched through your database and found many helpful suggestions,
but I am not sure why mdrun successfully runs on some files but not
others. The protein files are pretty but I get the following results
when running mdrun. (Yesterday I tried attaching the files but they
made the email too big and it got returned)
ABPa1OUT.pdb fails (Number of grid cells is zero. Probably the system
and box collapsed.)
QBPq1OUT.pdb succeeds with errors (some bonds rotated more than 30 degrees)
GBPg1OUT.pdb succeeds
Also, the topology files for ABP and GBP are made using 1 file, while
the QBP topology file is made using 2 files. (when 2 files are used, I
edit the topol.top file to have the posre_A.itp and posre_B.itp files --
#include "posre_A.itp")
Here are the commands I'm running:
pdb2gmx -f file_name.pdb -o -p < input.txt
editconf -bt octahedron -f -o -c -d 0.7
genbox -cp conf.gro -cs -o -p
grompp -f -c out.gro -p -o
mdrun -s -o -c -g -e
This looks like a classic question for this mailing list. MD simulations
will not "just work" because there are many things that have to be just
right and it is prohibitively difficult to ensure that for infinitely
many possible starting structures. If you have a look at some
literature, you will see that nobody reports a strategy like the above.
The reasons are varied. Often, either before or after you solvate a
system, there are atoms that are too close together or far apart to
resemble a real physical system. These need to be relaxed with an energy
minimization stage, or you risk having the dynamics fail because things
are too rough. Next, the velocities that are generated by the solvation
routine aren't magically going to be realistic all of the time. The
generation is a stochastic process and simply won't generate a coherent
self-consistent ensemble. That only happens after you allow the system
to equilibrate for a while. You should check the progress and results of
these processes visually - gromacs comes with a simple visualization
routine n_gmx, and I also recommend VMD. Only once you think it's
equilibrated & thus its behaviour might be similar to a real physical
system, should you start "observing" the system.
Mark
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