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

Adwait Mevada adwait at imsc.res.in
Thu Nov 18 04:09:35 CET 2010

>>> Date: Wed, 17 Nov 2010 15:08:02 -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:
     >>>     <aANLkTikE4LsexaxkRGoPd7w38nqwn8_jaRkQc_fFngC7 at mail.gmail.com>
     >>> Content-Type: text/plain; charset=3DISO-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 (=3DNVE).
     >> 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=3DaMMa4o0CzxU
     >>>>>>> http://www.youtube.com/watch?v=3DUVksVaHcw8U
     >>>>>>> http://www.youtube.com/watch?v=3DxJu3NSkA3gU
     >>>>>>> http://www.youtube.com/watch?v=3DcdcyqnPY7D4
     >>>>>> 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  
     >>>>> 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 whe=
     >>>>> 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 =3D no" and set
     >>>>  all cutoffs
     >>>> to 0 to capture all intramolecular interactions.
     >>>> -Justin
     >> Justin as you suggested I set pbc=3Dno, but i could not set  
cutoff's to 0
     >> as grompp was giving an error saying rvdw>=3Drlist so i set  
cutoff for vd=
     >> 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 =3D angular  
removed an=
     >> 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 se=
     > you're using.  For vacuum, you should set all cutoffs (rvdw,  
rcoulomb, rli=
     > equal to zero.  I suspect that the reduced rvdw is masking the real  =20
     > underlying
     > physical instability.

     I set cutoffs to zero as you suggested but i find that the simulation =20
     now just resembles the simulation of which videos i have uploaded on =20
     youtube previously

     > As for the condensed phase parameters, sensible non-zero values of  =20
     > all cutoffs
     > would be required, per whatever force field you're using.
     > -Justin



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