[gmx-users] Re: nve run of carbon nanotube

Adwait Mevada adwait at imsc.res.in
Wed Nov 17 15:40:03 CET 2010


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> Today's Topics:
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>    1. Re: nve run of carbon nanotube (Vitaly Chaban)
>    2. question (Raymond)
>    3. Re: question (Mark Abraham)
>    4. Reg: pcoupling and ref_p (vinothkumar mohanakrishnan)
>
>
> ----------------------------------------------------------------------
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> Message: 1
> Date: Tue, 16 Nov 2010 23:48:39 -0500
> From: Vitaly Chaban <vvchaban at gmail.com>
> Subject: [gmx-users] Re: nve run of carbon nanotube
> To: gmx-users at gromacs.org
> Message-ID:
> 	<AANLkTin9LAiTrJhjbMyZ74dU2vgJAJ8NTw5Y5awXu==0 at mail.gmail.com>
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> I would not say that you tube rotates so vigorously to be
> suspicious... The tube is also very small. What about trying a bigger
> one, e.g. with about 1 000 atoms? It should be more inert, if you'd
> like it to be such.
ok. I will do that and tell you what happens.
>
>> hope this might be useful:
>> they are top and sideviews
>> http://www.youtube.com/watch?v=aMMa4o0CzxU
>> http://www.youtube.com/watch?v=UVksVaHcw8U
>> http://www.youtube.com/watch?v=xJu3NSkA3gU
>> http://www.youtube.com/watch?v=cdcyqnPY7D4
>
> So, now the problem becomes why NVE simulation does not preserve
> system energy. I did not find above what method you used (MDP file)
> for the LJ interactions. I believe the problem is someplace around
> this point.
I do not get you, surely the itp & top files will have the information  
regarding
the LJ interactions. As far as i remember for C-C interactions I have  
C6 and C12 interaction mentioned in [non_bond param] section and also  
when defining the atom type C I have used the same parameter values,  
is there anything else i have to take into consideration besides that?
-Adwait
>
> --
> Dr. Vitaly Chaban
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 17 Nov 2010 14:52:48 +0800
> From: "Raymond" <3609746 at sina.com>
> Subject: [gmx-users] question
> To: "gmx-users" <gmx-users at gromacs.org>
> Message-ID: <201011171452473369164 at sina.com>
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> Message: 3
> Date: Wed, 17 Nov 2010 19:26:46 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] question
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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> On 17/11/2010 5:52 PM, Raymond wrote:
>> Why my rdf is larger than 1 in the long range
>> 2010-11-17
>> ------------------------------------------------------------------------
>> Raymond
>
> Probably because you did not measure what you thought you measured :-)
>
> Mark
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> Message: 4
> Date: Wed, 17 Nov 2010 14:08:54 +0530
> From: vinothkumar mohanakrishnan <kmvinoth at gmail.com>
> Subject: [gmx-users] Reg: pcoupling and ref_p
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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> Hi Gromacians
>
> I have created two liquid-liquid interfaces by combining three
> (DCE-Water-DCE) boxes. I want to calculate the Interfacial surface tension
> by using the surface tension option in Gromacs.
> I know that I need to give two values for ref_p one for xy and other for z.
> it was said in the manual that the "first value should be reference surface
> tension times the number of surfaces".what does it mean? what is this
> reference surface tension and what value i should put to calculate the
> surface tension? i know that the ref_p for z should be 1 bar (correct me if
> i am wrong) Further more how come ref_p unit will be bar nm for xy and for z
> it will be bar? any help is highly appreciated.
>
> Regards
> Vinoth
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-Adwait

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