Fw: [gmx-users] GROMOS87 and CHARMM27

[Shima Arasteh]

One more question:
But what about of using the potential surface?
In fact, I want to use the results of modeling in umbrella sampling. Is it possible?

Thanks in advance,
Shima 



________________________________
 From: Peter C. Lai <pcl at uab.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, April 16, 2012 9:50 PM
Subject: Re: [gmx-users] GROMOS87 and CHARMM27
 
On 2012-04-16 10:14:01AM -0700, Shima Arasteh wrote:
> So, I can not use the coordinates of the output files of gromos runs. Right?

You can but you may need to rename the atoms for each residue for pdb2gmx
to work.

> 
> 
> ________________________________
>  From: Peter C. Lai <pcl at uab.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
> Sent: Monday, April 16, 2012 8:23 PM
> Subject: Re: [gmx-users] GROMOS87 and CHARMM27
>  
> On 2012-04-16 08:26:00AM -0700, Shima Arasteh wrote:
> > Dear GROMACS users,
> > 
> > I reproduced the results of a protein-membrane system by using force field GROMOSE87. This protein forms ion channel in membrane.
> > Now if I wanna study
 the ion conduction through this channel using force field CHARMM27 in umbrella sampling method, is it possible? Can I use the results of the system simulation which has been derived by GROMOS87?
> 
> By definition, switching to a different forcefield like that usually requires 
> the regeneration of the system's topology, so your new system will be 
> different from your old one anyway. In addition, you may need to rename the 
> atoms in the coordinate files obtained from previous gromos runs to match 
> those in the charmm27 residue files.
> 
> -- 
> ==================================================================
> Peter C. Lai            | University of Alabama-Birmingham
> Programmer/Analyst        | KAUL 752A
> Genetics, Div. of Research    | 705 South 20th Street
> pcl at uab.edu            | Birmingham AL 35294-4461
> (205) 690-0808            |
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-- 
==================================================================
Peter C. Lai            | University of Alabama-Birmingham
Programmer/Analyst        | KAUL 752A
Genetics, Div. of Research    | 705 South 20th Street
pcl at uab.edu            | Birmingham AL 35294-4461
(205) 690-0808            |
==================================================================

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