[gmx-users] GROMOS87 and CHARMM27
Justin A. Lemkul
jalemkul at vt.edu
Wed May 2 16:32:59 CEST 2012
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 <jalemkul at vt.edu>
> *To:* Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS
> users <gmx-users at 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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> > *To:* Shima Arasteh <shima_arasteh2001 at yahoo.com
> <mailto:shima_arasteh2001 at yahoo.com>>; Discussion list for GROMACS
> > users <gmx-users at gromacs.org <mailto:gmx-users at 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 <pcl at uab.edu <mailto:pcl at uab.edu> <mailto:pcl at uab.edu
> <mailto:pcl at uab.edu>>>
> > > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> > <mailto:gmx-users at gromacs.org <mailto:gmx-users at 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 <pcl at uab.edu <mailto:pcl at uab.edu> <mailto:pcl at uab.edu
> <mailto:pcl at uab.edu>> <mailto:pcl at uab.edu <mailto:pcl at uab.edu>
> > <mailto:pcl at uab.edu <mailto:pcl at uab.edu>>>>
> > > > To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> > <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > > <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto: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 <mailto:pcl at uab.edu> <mailto:pcl at uab.edu
> <mailto:pcl at uab.edu>> <mailto:pcl at uab.edu <mailto:pcl at uab.edu>
> <mailto:pcl at uab.edu <mailto:pcl at 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
> > > pcl at uab.edu <mailto:pcl at uab.edu> <mailto:pcl at uab.edu <mailto:pcl at uab.edu>>
> <mailto:pcl at uab.edu <mailto:pcl at uab.edu> <mailto:pcl at uab.edu
> <mailto:pcl at 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
>
> ========================================
>
>
--
========================================
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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