[gmx-users] GROMOS87 and CHARMM27

Wed May 2 15:04:13 CEST 2012

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>
> *To:* Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS
> users <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>>
>  > *To:* Discussion list for GROMACS users <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>>>
>  > > 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 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>>
> | 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>> |
> 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

========================================