Thomas Piggot wrote:
Jochen thanks for your help.
That was what I was afraid of you saying. Oh well, at least this will
hopefully provide a useful reference so somebody doesn't make this
same mistake.
On a side note I noticed a couple of small issues with g_wham. Firstly
the -wcorr option says Input, opt. not Output, opt as I assume it
should be.
Ah thanks. I'll correct that soon.
Also when using -min and -max with the -noauto option, the program
quits with the error:
Fatal error:
With -auto, do not give -min or -max
Ok, I guess I never checked that case. But as you point out, you don't
have to use -noauto when providing min and max, the auto is switched off
automatically.
Thanks for the feedback,
Jochen
This is not a problem as with -min and -max (without specifying
-noauto) g_wham switches automatically switches auto off, but I
assumed that using -min and -max the -noauto option would have been
the 'correct' way to do this.
Cheers
Tom
Jochen Hub wrote:
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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