[gmx-users] Regarding use of g_x2top utility in Gromacs
rakesh.pant at students.iiserpune.ac.in
Sat Nov 25 21:22:23 CET 2017
I am trying to use it for graphene oxide (layer), then what would be a
better way if not g_x2top.
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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 A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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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
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