On 5/2/12 12:21 AM, Shima Arasteh wrote:
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?
Structures are force field agnostic. You can process them with whatever force
field you like. If the structure you want to simulate with CHARMM was previous
produced by Gromos87 (as I suspect, from looking at the thread below) then you
will definitely need to run for some additional time. The force field is
different and thus you need to re-equilibrate the system (at the very least)
under the new parameters.
-Justin
Thanks,
Shima
--------------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS
users <gmx-users@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 <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 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> <mailto:p...@uab.edu
<mailto:p...@uab.edu>>>
> > To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> <mailto: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> <mailto:p...@uab.edu
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> > (205) 690-0808 |
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> >
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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> <mailto: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
========================================
--
========================================
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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