Dear gmxers,
I want to analyze the non-traditional hydrogen bonds like C-H...O. To my
best knowledge, the g_hbond code can be used for traditional hydrogen bonds
but not for our case. One possible solution is to modify the g_hbond code
to include the non-traditional hydrogen bonds. However, the
On 2013-06-30 11:34, Wu Chaofu wrote:
Dear gmxers,
I want to analyze the non-traditional hydrogen bonds like C-H...O. To my
best knowledge, the g_hbond code can be used for traditional hydrogen bonds
but not for our case. One possible solution is to modify the g_hbond code
to include the
If you use periodic boundary conditions, there is no need that the
protein stays at one side of the box.
For the pulling simulation: Read the chapters 6.4 (explains the
pull-code) and 7.3.21 (explains the mdp-paramters).
Additional information you an also get from Justin Tutorial for Umbrella
Hi,
When I convert FF parameters from OPLS (in Gromacs) to Charmm, I divide
bond and angle force constants, i.e., Kb and Ktheta, by 836.8 and 8.368.
However, parameters for tip3p water do not convert properly in this ways.
For example, Kb = 502416.0 kJ/mol/nm^2 for OW-HW in Gromacs and 450.0
On 6/30/13 12:11 PM, Hyunjin Kim wrote:
Hi,
When I convert FF parameters from OPLS (in Gromacs) to Charmm, I divide
bond and angle force constants, i.e., Kb and Ktheta, by 836.8 and 8.368.
However, parameters for tip3p water do not convert properly in this ways.
For example, Kb = 502416.0
Hi Ankita,
The fie contains the eigenvectors as
x1 y1 z1
x2 y2 z2
...
xN yN zN
Hope it helps,
Tsjerk
On Mon, Jul 1, 2013 at 1:38 AM, Ankita naithani ankitanaith...@gmail.comwrote:
Hi,
I wanted to know the exact format of covariance.dat file as generated by
g_covar during covariance
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