Den 2018-06-02 kl. 11:06, skrev sp...@iacs.res.in:
Hi all
I am doing simulation of DNA molecule. I want to calculate groove width of
DNA in GROMACS. How to do this? Someone please help.
Thanks
Sunipa
Just out of curiosity, what does that tell you? I understand it may be
interesting for
Curves+ and 3DNA are standard tools for getting helical parameters. You
can find them pretty easily on Google.
Gregory
On 6/2/2018 5:06 AM, sp...@iacs.res.in wrote:
Hi all
I am doing simulation of DNA molecule. I want to calculate groove
width of
DNA in GROMACS. How to do this? Someone
This requires custom twisting analysis tools that Gromacs does not have
built-in, but one could implement them, there are many papers on the
subject. Also, a simple google search reveals http://curvesplus.bsc.es/
with downloads and documentation.
Alex
On 6/2/2018 3:06 AM, sp...@iacs.res.in
Hi all
I am doing simulation of DNA molecule. I want to calculate groove width of
DNA in GROMACS. How to do this? Someone please help.
Thanks
Sunipa
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Dear Justin
Many thanks for your reply.
My problem is not with the z axis. I use -g2 z for that as you mentioned.
I do not know how to define a vector for P-N vector.
Help me on this please.
Thanks in advance
Sincerely
Delara
On Wednesday, 30 May 2018, 16:19:18 GMT+4:30, Justin Lemkul
The cavity, which is due to negative pressure in the system, might imply
one of the two things:
The Box is too big for the system or that the MD simulation implodes the
system somehow. I have seen issues like these when the system is not well
minimized and has some obvious artefacts like "broken"
