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

[Vitaly Chaban]

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