On 5/2/12 10:30 AM, Shima Arasteh wrote:
Thanks for your reply.
What do you mean by running for some additional time?
You're introducing a new force field, which includes different representation of
atoms and a different potential energy function. You can't just take a
configuration generated by Gromos87, apply CHARMM27 parameters to it, and expect
continuity in the job. You need to re-equilibrate the structure under the new
parameters.
I guess,I have to modulate the structure from the first point. Right? I think
the results of last run using gromos is not beneficial at all, because the
parameters are different for sure.
Having little idea what you're doing, I'll tend to agree.
-Justin
Cheers,
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:* Wednesday, May 2, 2012 5:34 PM
*Subject:* Re: [gmx-users] GROMOS87 and CHARMM27
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 <mailto:jalem...@vt.edu>>
> *To:* Shima Arasteh <shima_arasteh2...@yahoo.com
<mailto:shima_arasteh2...@yahoo.com>>; Discussion list for GROMACS
> users <gmx-users@gromacs.org <mailto: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>
<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 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>> <mailto: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>>
> > <mailto: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
<mailto:p...@uab.edu>> <mailto: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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> > --
> > ==================================================================
> > Peter C. Lai | University of Alabama-Birmingham
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> > Genetics, Div. of Research | 705 South 20th Street
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> > ==================================================================
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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
========================================
--
========================================
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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