Adwait Mevada wrote:
Quoting [email protected]:
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Message: 4
Date: Wed, 17 Nov 2010 15:08:02 -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
Also, as far as I understand, before NVE simulation, one should
equilibrate the system in the NVT ensemble (at the desired T) and
only then switch off T-coupling (=NVE).
so are you suggesting that for the parameters I want to test I should
fix a temp say 300K, then simulate it (in vaccum) with NVT, see if the
physical variables equilibrate around experimental values and then go
switch of T-coupling?
Vitaly Chaban
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
You didn't set "vdwtype" in your .mdp file, but in this case it
should default
to "cutoff," which I don't think is a problem. What might be an
issue is your
treatment of PBC. If your box is somewhat small, your system will
experience
repulsion from forces derived from periodic copies of your molecule.
The proper
approach for a vacuum simulation would be to set "pbc = no" and set
all cutoffs
to 0 to capture all intramolecular interactions.
-Justin
Justin as you suggested I set pbc=no, but i could not set cutoff's to 0
as grompp was giving an error saying rvdw>=rlist so i set cutoff for vdw
to 0.4 instead of 1 which resulted in greatly reduced perturbations in
the geometry to the extent that the carbon nanotube retained its
cylindrical structure. The temprature was 4K and T.E. of the system were
11 as computed
by g_energy with LJ being -0.69. setting comm_mode = angular removed any
rotation about x axis for the system
I also tried the same thing with a large nanotube containing 1000 atoms
as suggested by Vitaly, and his suggestion also works out i do not find
distortions in the geometry except that being a long narrow tube it
flutuates
along its length, which is fine i suppose.
What i wonder is why reduction in rvdw helps in reducing the fluction?
and also now if i want to put this carbon nanotube in water will using
this parameter set suffice or i will have to make changes so that it is
stable in
water either in NVT or NPT ensemble?
Making ad hoc changes to rvdw will break whatever force field parameter set
you're using. For vacuum, you should set all cutoffs (rvdw, rcoulomb, rlist)
equal to zero. I suspect that the reduced rvdw is masking the real underlying
physical instability.
As for the condensed phase parameters, sensible non-zero values of all cutoffs
would be required, per whatever force field you're using.
-Justin
-Adwait
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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