Nilesh Dhumal wrote:
My box size is 4.5 4.5 4.5 (in nm)90 90 90
Seems awfully large for only 128 waters. I just wonder if the box is distorting
during the simulation such that the periodic distance becomes the reference
distance, hence the switch between positive and negative distances. This
concept is discussed in the tutorial I linked before.
My boss want to see the natue of plot before going for sampling.
You can't generate a PMF curve from a single simulation. Any resulting plot
will be completely useless. Please reference the literature about the method,
as well as the simple explanation I provide in the tutorial.
-Justin
Nilesh
On Wed, December 29, 2010 1:04 pm, Justin A. Lemkul wrote:
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_Sam
pling
-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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting! Please don't post (un)subscribe requests to the list. Use
the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post?
Read
http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org. Can't post?
Read
http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
