[gmx-users] GROMOS87 and CHARMM27
shima_arasteh2001 at yahoo.com
Mon Apr 16 19:14:01 CEST 2012
So, I can not use the coordinates of the output files of gromos runs. Right?
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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