lammps lammps wrote:
Dear all,
It is the first time that I use gromacs 4.04 to calculate PMF. I have
some question needed to be clarified.
1.
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; pull code for PMF
pull = Unbrella ;unbrella,constraint
pull_geometry = Distance ;distance
,direction,cylinder,position
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?
They do not have to be the same. The values set depend on how many data points
you want in the pullf.xvg and pullx.xvg files.
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?
The .tpr files used for the different sampling windows are passed to g_wham.
See g_wham -h for the details.
-Justin
3. What other thing I must take care of for calculation of PMF
Thanks in advance.
--
wende
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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