[gmx-users]Thanks!

[Yang Ye]

Hi, Zhang

It has different combinations as long as you are sure that
the "a" and "c" in (a exp (-br) - c exp (-dr) + qq/r) refer what you put 
in the last two numbers in atomtypes and nonbond_params. and exp(-br) 
and exp(-dr) are what you put in the table. I did my test for this.

Then, you may just put 1 and 1 or even 1 and 0 for LJ parameters. But if 
you use pairs, you got to also define 1-4 tables for LJ interactions 
(see 3.3's mdrun's online help).

Yang Ye

Junfang.Zhang at csiro.au wrote:

> Many thanks, Yangye.
>
>  
>
> I have got another question, and hope you can assist me.
>
>  
>
>If I apply the user defined potential which takes the form as follows
>
> (a exp (-br) - c exp (-dr) + qq/r) to describe the interactions 
> between K, H2O, and clay layer (which consists of SI,O, and OH groups).
>
>  
>
> Under the [ nonbond_params ] directive, I can give the interaction 
> parameters C6 and C12  between different atoms, for example, O and K, 
> SI and K, SI and H, etc. My question is under the [ atomtypes ], do I 
> have to give C6 and C12 for individual atom? If so, where to get these 
> values?
>
>  
>
>  
>
> [ atomtypes ]
>
> opls_115  1.00000       0.000       A         ?          ?
>
> opls_114  1.00000       0.000       A         ?          ?
>
> opls_113  1.00000       0.000       A         ?          ?
>
>  
>
> C4        1.00000       0.000          A         ?          ?
>
> SI        28.0800       1.200105     A          ?          ?
>
>  
>
> O1        15.99940      -0.80007    A          ?          ?
>
>  
>
> O2        15.99940      -0.71748    A          ?          ?
>
>  
>
>  SI    28.08000       0.000            A          ?          ?
>
>  
>
> [ nonbond_params ]
>
>  C4   opls_113    1      3.704000E-01   1.1359277e+00
>
>  SI   opls_114    1      0.00000E+00   0.00000E+00
>
>  SI   opls_113    1      0.62105E-02   0.76440E-05
>
>  
>
>  O    opls_113    1      0.25539500E-02   0.2512E-05
>
>  K    opls_113    1      0.2671000E-02    0.0000e+00
>
>  
>
>  
>
> With my best regards and thanks,
>
>  
>
>  
>
> Junfang
>
>  
>
> -----Original Message-----
> *From:* leafyoung81-group at yahoo.com [mailto:leafyoung81-group at yahoo.com]
> *Sent:* Tuesday, 3 January 2006 2:22 PM
> *To:* Zhang, Junfang (DPR, Clayton)
> *Subject:* Re: [gmx-users]Contradictory found on page 125/134 of 
> manual-3.2.pdf
>
>  
>
> Hi, Zhang
>
> This can be verified with table6-xx.xvg inside top directory. Shall be 
> the positive one.
>
> Yang Ye
>
> ----- Original Message ----
> From: Junfang.Zhang at csiro.au
> To: gmx-users at gromacs.org; leafyoung81-group at yahoo.com
> Sent: Tuesday, January 03, 2006 10:57:49 AM
> Subject: RE: [gmx-users]Contradictory found on page 125/134 of 
> manual-3.2.pdf
>
>
> Dear Yangye and Gromacs users
>
>  
>
> On page 125 of manual-3.2.pdf, it is stated that table.xvg has seven
>
> columns of table lookup data in the order: x, f(x), f^(2)(x), g(x), 
> g^(2)(x), h(x), h^(2)(x), but on page 134, it is mentioned that this 
> file should contain 7 columns: the x
>
> , f(x), -f^(2)(x), g(x), -g^(2)(x), h(x), -h^(2)(x). Can you please 
> let know which one is correct?
>
>  
>
> Happy new year to you all,
>
>  
>
> Junfang
>
>  
>
>  
>
>  
>
> -----Original Message-----
> *From:* gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Yang Ye
> *Sent:* Thursday, 22 December 2005 6:10 PM
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users]
>
>  
>
> Try use table (see manual 6.4.2). Note that there is new option 
> available in 3.3 that you can assign different table for the 
> interactions between different groups of atoms. Check 3.3's document 
> (share/html/online.html), section "mdp option".
>
> Yang Ye
>
> Junfang.Zhang at csiro.au <mailto:Junfang.Zhang at csiro.au> wrote:
>
>Dear Gromacs users,
>
> 
>
>If I use the MCY potential which takes the form as follows
>
>(a exp (-br) - c exp (-dr) + qq/r),
>
> 
>
>which source files in GROMACS do I need to modify?
>
> 
>
> 
>
>Thanks,
>
> 
>
>Junfang
>
> 
>
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> 
>
>  
>
>  
>
> -- 
> /Regards,/
> Yang Ye
> /Computational Biology Lab
> School of Biological Sciences
> Nanyang Technological University
> Singapore
> Tel: 6316-2884/
>

-- 
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/