[gmx-users] Regarding use of g_x2top utility in Gromacs

[Rakesh Pant]

Dear Justin,

I am trying to use it for graphene oxide (layer), then what would be a
better way if not g_x2top.

Thanks,



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On Sun, Nov 26, 2017 at 1:48 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/25/17 3:12 PM, Rakesh Pant wrote:
>
>> Dear All,
>>
>> How does the utility g_x2top works?
>> If we have similar connectivity in a molecule, then how will it read
>> different atom types. Suppose a C atom is connected to 4 bonds (3 carbon
>> atoms and 1 O atom, say in epoxy group) and similarly another C atom is
>> also connected to 4 atoms (3 C atoms and 1 O atom, but the different
>> functional group, e.g phenolic group). Both are present in the same
>> molecule, then how should we define both in the .n2t file so that g_x2top
>> reads both the atomtypes.
>>
>
> The only difference in that case might be bond lengths, though they may
> not be different enough to be distinguished (they would have to differ by
> at least 10% to be outside of the default tolerance). x2top is not a
> particularly smart program, and whatever it matches first will be what it
> writes to the topology. If you have some very complex molecule, this may
> not be a useful tool.
>
> -Justin
>
> --
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-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm