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=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
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 whe=
n
>>>>> 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=
w
>> 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=
y
>> 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=
t
> you're using. For vacuum, you should set all cutoffs (rvdw,
rcoulomb, rli=
st)
> 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
-Adwait
-Adwait
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