Nilesh Dhumal wrote:
I have a system with 128 water molecules and a ion pair of ionic liquids
i.e. one cation and one anion.
the reaction corrdination is the distance between cation and anion.
Initial distance between cation-anion is 0.8 nm.
What is the size of the smallest box vector?
I have pasted some part of md file
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = NO ; define initial COM distance > 0
;reftype = com
pull_ngroups = 1
pull_group0 = EMI
pull_group1 = ETS
pull_init1 = 0.0
pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
I run the simulation for 2ns then I run g_wham.
You're only running one simulation? That's not appropriate for umbrella
sampling.
http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
-Justin
I more interested in structure where caion and anion are close ~0.4 nm.
After ploting PMF I found that I have -ve value of z.
NIlesh
On Wed, December 29, 2010 12:51 pm, Justin A. Lemkul wrote:
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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--
========================================
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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