Thomas Piggot wrote:
Hi,
I am trying to construct a PMF profile for a phosphate ion passing
through a membrane protein using umbrella sampling with GROMACS 4.0.5.
I have performed the umbrella sampling simulations using the following
mdp options and I am now attempting to construct the PMF using g_wham.
; Pull code
pull = umbrella ; do umbrella sampling
pull_geometry = distance ; can't get PMF with direction
Hi Tom,
if you want to distinguish between above and below,
pull_geometry=position would have been your choice. What I would do now
is to run g_wham twice with only the histograms from below and a second
time only with the histograms from above your reference. YOu'll have to
make appropriate tpr-files.dat and pullx-files.dat input files. Note
however, that the PMF very close to your reference will be ill-defined
since the pull code checked the distance to the reference and not the
z-coordinate. Therefore I would remove simulations in which the ion was
sometimes above and sometimes below the reference.
To ge the full PMF along the z-axis (which is what you probably want)
you'll have to do the simulation again (with pull_geometry=position) I'm
afraid.
I hope this helps,
Jochen
pull_dim = N N Y ; just in the z
pull_start = yes ; add com to pull_init1
pull_ngroups = 1 ; no. of groups to pull
pull_group0 = Protein ; reference group
pull_group1 = PO4 ; pull group
pull_vec1 = 0 0 0 ;
pull_init1 = 0 ;
pull_rate1 = 0.0 ; no change in ref position
pull_k1 = 1000 ; force constant for restraint
pull_nstxout = 1000 ; every 2 ps
pull_nstfout = 1000 ; every 2 ps
The problem is that when running g_wham (using the following command)
g_wham correctly reads all of the tpr and pullx files, however the
data for the windows above and below the reference atom (the middle
atom of the protein) are both included in the same part of the PMF
profile.
g_wham_4.0.5 -ix -it -cycl weighted -b 2000
I assume that this is occuring due to the pull_geometry = distance
option, as the distance to the reference does not matter if the ion is
above or below the reference?
So my question is: Is there a way to construct the complete PMF
profile with the simulations I have already run?
I should also mention that I have tried using the -min and -max
options with g_wham (rather than the auto determination of the
boundaries) but this just produces outputs that have all the values as
nan. I have also tried using g_wham 4.0.7 but with exactly the same
issues ,as well as using the pullf.xvg files as input to g_wham.
I apologise if I am missing something obvious (or doing something
silly!) but any help would be greatly appreciated.
Cheers
Tom
--
---------------------------------------------------
Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
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