On 1/07/2012 7:31 AM, SatyaK wrote:
Hello All,
I am working on DNA simulations using GROMACS
Question: I created A.gro file that has DNA molecule and water molecules
within a box using GROMACS. I want to create a cylinder around the DNA so
that I can place some ions, or, compute axis of DNA
On 1/07/2012 1:16 AM, Shima Arasteh wrote:
Hi dear gmx friends,
I have a C atom which its neighbors are N, O, H atoms and then sp2
hybridization. I wanna add this atom to the CHARMM36, but I don't know its atom
type.
Neither can we. Your description could be of H-C(=O)-NXY or H-C(=NX)-OY.
On 30/06/2012 10:18 PM, ms wrote:
On 29/06/12 19:59, Justin A. Lemkul wrote:
Wouldn't it be nice to create a table of "standard settings" for each
forcefield
in the gmx documentation (with lit references of course)?
Well, anyone is welcome to submit anything they feel would be
useful... ;)
On 28/06/2012 8:07 PM, Raj wrote:
during the simulation. I tried g_chi to obtain chi1 and chi2 values at the
end I'm getting the plot withe values ranges from -180 to 180 . But in
papers people have reported
in 360 degree how can i get the data. Please give me suggestions
The data is periodic
On 7/1/12 12:02 AM, Raj wrote:
Dear Justin,
I've tried what you have suggested. I have used the pull code and gave 4
amino acid residues as a reference group. The location of the groups are one
below the ligand (in the protein core) and 3 were on the above ( towards the
active site gorge). Whe
Hi,
Suppose that I have a system of benzene molecules (in reality, my system is
more complicated, but for my question, it will be simpler to consider just
an ensemble of benzene molecules).
I would like to find a vector normal (i.e., perpendicular) to the plane of
each benzene molecule in my sy
On 2/07/2012 6:50 AM, Andrew DeYoung wrote:
Hi,
Suppose that I have a system of benzene molecules (in reality, my system is
more complicated, but for my question, it will be simpler to consider just
an ensemble of benzene molecules).
I would like to find a vector normal (i.e., perpendicular) to
On 2/07/2012 11:51 AM, Mark Abraham wrote:
On 2/07/2012 6:50 AM, Andrew DeYoung wrote:
Hi,
Suppose that I have a system of benzene molecules (in reality, my
system is
more complicated, but for my question, it will be simpler to consider
just
an ensemble of benzene molecules).
I would like t
Dear Mark,
Thanks for your reply.. can you suggest me how i can take the plot with 0 to
360 angle. I've tried periodic of g_chi with -all option to generate the
chi1/chi2 plot for the each and every amino acid residue but i couldnt do it
properly can you suggest on this. Thanks in advance
--
View
On 2/07/2012 12:20 PM, Raj wrote:
Dear Mark,
Thanks for your reply.. can you suggest me how i can take the plot with 0 to
360 angle. I've tried periodic of g_chi with -all option to generate the
chi1/chi2 plot for the each and every amino acid residue but i couldnt do it
properly can you suggest
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