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Today's Topics:
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 <[email protected]>
Subject: [gmx-users] Re: nve run of carbon nanotube
To: [email protected]
Message-ID:
<[email protected]>
Content-Type: text/plain; charset=ISO-8859-1
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
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Message: 2
Date: Wed, 17 Nov 2010 14:52:48 +0800
From: "Raymond" <[email protected]>
Subject: [gmx-users] question
To: "gmx-users" <[email protected]>
Message-ID: <[email protected]>
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Message: 3
Date: Wed, 17 Nov 2010 19:26:46 +1100
From: Mark Abraham <[email protected]>
Subject: Re: [gmx-users] question
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
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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 <[email protected]>
Subject: [gmx-users] Reg: pcoupling and ref_p
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
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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