Hii
Thank you for your help. It is working successfully.
Sunipa
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On Mon, Jun 4, 2018 at 1:10 PM, wrote:
> Hii
>> I have tried installation of do_x3dna in ubuntu system following the
>> instructions given in the link. Installation done successfully then I
>> have written the path of do_x3dna in .bashrc file(export
>> do_x3dna=/usr/local/do_x3dna/bin/) and
- Message from rajendra kumar -
Date: Mon, 4 Jun 2018 12:23:56 +0200
From: rajendra kumar
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Groove width
To: Discussion list for GROMACS users
I am doing simulation of DNA molecule. I want to calculate groove
Hii
I have tried installation of do_x3dna in ubuntu system following the
instructions given in the link. Installation done successfully then I
have written the path of do_x3dna in .bashrc file(export
do_x3dna=/usr/local/do_x3dna/bin/) and source the file source ~/.bashrc.
Then I tried doing
>
>
> I am doing simulation of DNA molecule. I want to calculate groove width of
> DNA in GROMACS. How to do this? Someone please help.
>
>
You may use do_x3dna (http://do-x3dna.readthedocs.io). It uses 3DNA in
background and works with GROMACS files. Package also includes tools to
analyze the
Hii David
I want to see if there is any change in the groove width in presence
of different solvents. I thing this can give me some information of DNA
structural change if it is happening in that particular solvent.
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Thank you for your suggestion. This is a new thing I am learning.
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Hi,
> On Jun 2, 2018, at 9:22 PM, David van der Spoel wrote:
>
> 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
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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