[gmx-users] protein-SWCNT md simulation

[Justin Lemkul]

On 2/4/13 12:21 AM, Atila Petrosian wrote:
> Dear Justin
>
> Thanks for your reply.
>
>>   2. Create topology for other elements using g_x2top or other external software
> and convert them to .itp
>
> Can I use PRODRG server to creat topology for cnt?
>

Doubtful.  PRODRG produces topologies compatible with Gromos96 43A1 (with manual 
modification) and doesn't handle periodic molecules, so if you have an infinite 
CNT, it won't work.  You should also base the choice of force field on the 
quality of its results, not the easy availability of web servers.

> -----------------------------------------
>
> Parameters of amber 03 which I used are as follows:
>
>
> ffcnt.atp file >>>
>
> CA                12.01000	; sp2 C pure aromatic (benzene)
>
>
> ffcnt.n2t file >>>
>
> C    CA    0.00    12.01000  3    C 0.141   C 0.141   C 0.141
> C    CA    0.00    12.01000  1    C 0.141
>
>
> forcefield.itp file >>>
>
> #define _FF_cnt
> [ defaults ]
> ; nbfunc	comb-rule	gen-pairs	fudgeLJ	fudgeQQ
> 1	2	yes	1.0	1.0
>
> #include "ffcntnonbon.itp"
> #include "ffcntbon.itp"
>
>
> ffcntbon.itp file >>>
>
> [ bondtypes ]
> ; i	j	func	b0	kb
> CA  CA         1    0.14000   392459.2
>
> [ angletypes ]
> ; i	j	k	func	th0	cth
> CA  CA  CA           1   120.000    527.184
>
> [ dihedraltypes ]
> ; i	j	k	l	func   phase      kd      pn
> CA  CA  CA  CT       4      180.00     4.60240     2
>
>
> ffcntnonbon.itp file >>>
>
> [ atomtypes ]
> ;name	at.num	mass	charge	ptype	sigma	epsi
> CA           6      12.01    0.0000  A   3.39967e-01  3.59824e-01
>
> ----------------------------------------------
>
> Please check content of these file. If there is problem, please tell me.
>

The problem is in declaring a separate force field for one molecule in the 
system which, as we have established, is already adequately described by the 
Amber03 force field that you want to use.  I see no need whatsoever to create a 
new force field, and furthermore one that has fudge values that conflict with 
the parent.

Bottom line in my mind: operate completely within Amber03.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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