[gmx-users] GROMOS87 and CHARMM27
Justin A. Lemkul
jalemkul at vt.edu
Mon Apr 16 19:20:09 CEST 2012
Shima Arasteh wrote:
> So, I can not use the coordinates of the output files of gromos runs. Right?
Not without significant modification of names, presence of H atoms, etc. You'll
need to regenerate a suitable topology, as has been said, and then run thorough
equilibration under the new force field.
> *From:* Peter C. Lai <pcl at uab.edu>
> *To:* Discussion list for GROMACS users <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
> 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> | Birmingham AL 35294-4461
> (205) 690-0808 |
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> 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>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users