[gmx-users] GROMOS87 and CHARMM27

[Shima Arasteh]

Dear Justin,
I don't want to compare the forcefields results.
Yes, Iwant to use some old information in conjunction with something new.
In fact, I have to regenerate a structure, which has modulated using gmx.ff. After it, I am going to study it using umbrella sampling technique. I want to do it using charmm27. I want to know if it is possible? Is it correct that I use the results of the job done by gmx? Or I need to repeat the job using charmm?

Thanks,
Shima


________________________________
 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, May 1, 2012 9:44 PM
Subject: Re: Fw: [gmx-users] GROMOS87 and CHARMM27
 


On 5/1/12 1:08 PM, Shima Arasteh wrote:
>
>
> 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?
>

I, for one, am not clear what you are asking.  Are you trying to compare force 
field results?  Build a system based off another?  Use some old information in 
conjunction with something new (i.e. force field mixing, which is a bad idea)?

-Justin

> 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 <mailto:pcl at uab.edu>>
>  > To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto: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 <mailto: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 <mailto:pcl at uab.edu> | Birmingham AL 35294-4461
> (205) 690-0808 |
> ==================================================================
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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