[gmx-users] GROMOS87 and CHARMM27

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed May 2 16:40:20 CEST 2012 

Thanks for your kind reply .
Sincerely,
Shima



________________________________
 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Wednesday, May 2, 2012 7:02 PM
Subject: Re: [gmx-users] GROMOS87 and CHARMM27
 


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 |
>  > > > ==================================================================
>  > > >
>  > > > --
>  > > > gmx-users mailing list 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>>>
>  > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  > > > Please search the archive at
>  > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>  > > > Please don't post (un)subscribe requests to the list. Use the
>  > > > www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
>  > <mailto:gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>>
>  > > <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>>.
>  > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  > >
>  > > > --
>  > > > gmx-users mailing list 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>>>
>  > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  > > > Please search the archive at
>  > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>  > > > Please don't post (un)subscribe requests to the list. Use the
>  > > > www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
>  > <mailto:gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>>
>  > > <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>>.
>  > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  > >
>  > >
>  > > --
>  > > ==================================================================
>  > > 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 |
>  > > ==================================================================
>  > >
>  > > --
>  > > gmx-users mailing list 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>>>
>  > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  > > Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search
>  > > before posting!
>  > > Please don't post (un)subscribe requests to the list. Use the
>  > > www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
>  > <mailto:gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>>
>  > > <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>>.
>  > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  > >
>  > >
>  > >
>  > >
>  > >
>  > >
>  >
>  > --
>  > ========================================
>  >
>  > 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

========================================
-- 
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120502/8f0c9c05/attachment.html>

More information about the gromacs.org_gmx-users mailing list