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 simulation? If you have a better strategy to compute 2d-pmf with gromacs to share with me, I would really appreciate it. Best, Yuan -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
