Nilesh Dhumal wrote:
If I am geting -ve value if z in g_wham then zero is my initial distance
or reference distance.
That means your pull group has a coordinate that is negative with respect to the
reference group at some point during (at least) one of the umbrella sampling
windows. Zero, in this case, corresponds to an equivalent coordinate in the
pull dimension.
Without a substantially more detailed description of your system and what you've
done, you're unlikely to get anything more helpful.
-Justin
Nilesh
On Sat, December 11, 2010 9:43 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I trying to run umbrella sampling simulation for system.
After running g_wham command I am geting some negative value of z along
x axis.
g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kcal
Can any one tell why I am geting -ve value or what is the significance
of this.
That means the coordinate of your pull group is less than that of your
reference group along the reaction coordinate. The reason for that
depends on how you constructed your pull and reference groups and how you
carried out the umbrella sampling.
-Justin
Nilesh
--
========================================
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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--
========================================
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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