On 11/25/14 1:23 AM, Sathish Kumar wrote:
Hai gromacs users,
Can we use the direction-periodic mdp option
while running the samplling of windows instead of distance. The distance
option was giving error that
Distance of pull group 1 (15.017257 nm) is larger than
Hai gromacs users,
Can we use the direction-periodic mdp option
while running the samplling of windows instead of distance. The distance
option was giving error that
Distance of pull group 1 (15.017257 nm) is larger than 0.49 times the box
size (15.033495) .
So, for
On 10/30/14 1:19 AM, Sathish Kumar wrote:
Dear gromacs-users,
I have run the umbrella sampling with the help of
tutorial of justin. In my system rna is binding with gold nanoparticle. To
find out the binding energy, i run the umbrella sampling using the space
0.1 nm
Dear gromacs-users,
I have run the umbrella sampling with the help of
tutorial of justin. In my system rna is binding with gold nanoparticle. To
find out the binding energy, i run the umbrella sampling using the space
0.1 nm and i got total 79 configurations, each
Hi. Does that mean the umbrella don't overlap enough at those z ?
Can you make an overlay plot of the histograms of each umbrella?
On Mon, Oct 13, 2014 at 1:54 AM, Sathish Kumar sathishk...@gmail.com
wrote:
Dear gromacs usres,
I have run the umbrella sampling with the help of tutorial of
Yes, it means what you say.
I would decrease the number of bins.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Mon, Oct 13, 2014 at 12:47 PM, Johnny Lu johnny.lu...@gmail.com wrote:
Hi. Does that mean the umbrella don't overlap enough at those z ?
Can you make an overlay plot of the
Hai
Yes, I have ploted the histogram, all windows are merged..please
check this histo.jpg file attached to the below link.
https://www.dropbox.com/s/ndl0w250dnawmib/histogram.jpg?dl=0
On Mon, Oct 13, 2014 at 3:47 AM, Johnny Lu johnny.lu...@gmail.com wrote:
Hi. Does that mean the
I am not able to find wheather the windows are overlaped or not. Please
help me in this.
Thanks.
On Mon, Oct 13, 2014 at 10:05 AM, Sathish Kumar sathishk...@gmail.com
wrote:
Hai
Yes, I have ploted the histogram, all windows are merged..please
check this histo.jpg file attached to the
On 10/13/14 1:08 PM, Sathish Kumar wrote:
I am not able to find wheather the windows are overlaped or not. Please
help me in this.
You've got a gap in the sampling exactly where g_wham tells you. The histograms
show this. You either need more windows or a different force constant, or
Hai
I have decreased the number of bins=50 and i have not get the
previously mentioned warnings. Still, the profile.xvg is looking like below
2.148184e+000.00e+00
2.300988e+000.00e+00
2.453792e+000.00e+00
2.606596e+000.00e+00
2.759400e+000.00e+00
Dear gromacs usres,
I have run the umbrella sampling with the help of tutorial of justin. In
my system rna is binding with gold nanoparticle. To find out the binding
energy, i run the umbrella sampling using the space 0.1 nm and i got total
79 configurations, each configuration was run for 5 ns.
On 9/29/14 10:09 AM, Sathish Kumar wrote:
Dear gromacs usres,
I have run the umbrella sampling with the help of tutorial of justinIn
my system rna is binding with gold nanoparticle...to find out the binding
energy i run the umbrella sampling using the space 0.2 nm and i got total
59
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