[gmx-users] GROMOS87 and CHARMM27

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 16 19:20:09 CEST 2012

Shima Arasteh wrote:
> So, I can not use the coordinates of the output files of gromos runs. Right?

Not without significant modification of names, presence of H atoms, etc.  You'll 
need to regenerate a suitable topology, as has been said, and then run thorough 
equilibration under the new force field.


> ------------------------------------------------------------------------
> *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
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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