[gmx-users] How to calculate the PMF?

lammps lammps lammp2forum at gmail.com
Wed Dec 9 15:31:55 CET 2009

Dear all,

It is the first time that I use gromacs 4.04 to calculate PMF. I have some
question needed to be clarified.

; pull code for PMF
pull                            = Unbrella        ;unbrella,constraint
pull_geometry             = Distance        ;distance
pull_dim                     = N N Y
pull_group0                 = DPPC
pull_group1                 = DEN
pull_nstxout                = 100
pull_nstfout                 = 100
pull_init1                     = 3.8
pull_k1                       = 1000

Is there any relationship between the steps for pull_nstxout and
pull_nsfout. Must they be the same( e.g. 100, 100)? How to choose them?

2. It seems that there are only two output file: pullx.xvg and pullf.xvg. Is
it right?  are there other files for the input of g_wham?

3. What other thing I must take care of for calculation of PMF

Thanks in advance.

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