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 <p...@uab.edu>
*To:* Discussion list for GROMACS users <gmx-users@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 <p...@uab.edu <mailto:p...@uab.edu>>
> To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto: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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==================================================================
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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