[gmx-users] 2d-pmf with plumed gromacs

Yuan Hu yuanhu at udel.edu
Thu Apr 18 01:08:23 CEST 2013

 Dear gromacs user,

We want to compute a 2d-PMF for a peptide translocating into a coarse
grained water lipid system.
We find gromacs patched with plumed could allow us to run 2d umbrella
sampling, so we install  gromacs 4.6.1 with mpi support, and patch it with
plumed 1.3.

>From plumed documentation, they mentioned that  "Only NVT simulations are
supported because the contribution to the virial is not calculated."

Did anyone carry out a NPT simulation with PLUMED gromacs? Is there any
chance we can run a NPT simulation with PLUMED gromacs?
How much the error bar will be by using NPT ensamble for coarse grained

If you have a better strategy to compute 2d-pmf with gromacs to share with
me, I would really appreciate it.


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