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.
-Justin
------------------------------------------------------------------------
*From:* Peter C. Lai <p...@uab.edu>
*To:* Discussion list for GROMACS users <gmx-users@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
p...@uab.edu <mailto:p...@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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