[gmx-users] Re: Using Morse potentials with ENCAD force field

[Andy Shelley]

Using the parameters listed earlier I equalized my system after trying to
place the oxygen and nitrogen molecules evenly throughout my system.  The
result showed the nitrogen molecules fairly even throughout the system but
all the oxygen molecules on one side.  Any ideas on why the system might not
be equalizing out to an even distribution of oxygen by nitrogen?

Andy

It seems because your box should be a bit longer to succeed. Try to
enlarge the side (13.2 nm) length.


2008/8/21 Andy Shelley <robert.shelley at gmail.com>:
> No problem the term flattens is porbably not the best technical
> description.  A better one would be the cnt collapses.
>
> Andy
>
> On Thu, Aug 21, 2008 at 8:34 AM, Vitaly Chaban <chaban at univer.kharkov.ua>
> wrote:
>>
>> >
>> > Actually I think I am using the gromos force field. I have been using
>> > Christopher Stiles page as a guide to get started with using CNT
>> > http://cs86.com/CNSE/SWNT.htm. I realize now that all the modifications
>> > were
>> > made to ffgmx files.  So I believe I am using the gromos forcefield. Is
>> > the
>> > forcefield used defined by the parameters? I have added nonbonded
>> > parameters
>> > to ffgmxnb.itp as the following:
>> > [ nonboned_params ]
>> >   O    N    1 0.0069        1.4016E-05
>> >    O    O    1 0.0061        9.9676E-06
>> >    N    N    1 0.0076        1.8778E-05
>> >    C    O    1 0.0030        4.7908E-06
>> >    C    N    1 0.0033        6.5271E-06
>> >
>> > and the same for pairtypes
>> >  [ pairtypes ]
>> >    C    N    1  0.0033       6.5271E-06
>> >    C    O    1  0.0030       4.7908E-06
>> >    N    N    1  0.0076       1.8778E-05
>> >    O    O    1  0.0061       9.9676E-06
>> >    O    N    1  0.0069       1.4016E-05
>> >
>> > I have put just 200 nitrogen molecules in a 24.7nm x 24.7nm x 12.3nm
box
>> > with a 10,10 cnt length 12.3nm.  The nitrogen molecules appear to not
>> > even
>> > interact with the cnt but it still flattens.  Any ideas?
>> >
>>
>> Andy,
>>
>> Hi. Sorry for my English, what do you mean saying "cnt flattens"?
>>
>> Again, is everything right with your box side length. I mean if the
>> cnt fits in the box (the rim atoms)?
>>
>>
>> --
>> Vitaly V. Chaban
>> School of Chemistry
>> National University of Kharkiv
>> Svoboda sq., 4, Kharkiv 61077, Ukraine
>> email: chaban at univer.kharkov.ua
>> skype: vvchaban
>
>



--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban
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