[gmx-users] Free energy of solvation of large molecule

[Jernej Zidar]

Hi,
  I'm trying to calculate the free energy of solvation of a relatively
large polymer molecule (161 atoms). I went through the free energy
tutorial published on J. Lemkul's web page but when trying to apply
the same approach to my case, the simulations typically fail. The
files for one such case are here:
https://www.dropbox.com/s/z5z3ip767dgwloh/coul0.0.tar.gz

  I looked all over the internet to find a similar use case but most
people seem to have studied small organic molecules, which means
computing the solvation free energy for my molecule is far from
trivial.
  I understand I'll have to do simulations at many lambda points for
rather long periods of time but how to run them in a stable way?

Thanks in advance,
Jernej