[gmx-users] clayff forcefield

[G R]

On Wed, Aug 9, 2017 at 1:04 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. Re: clayff forcefield (Justin Lemkul)
>    2. (no subject) (Sorour Hasani)
>    3. Re: Generating topology file for a long polymer chain (Mahsa E)
>    4. convert .tpr to include energy groups (Tushar Ranjan Moharana)
>    5. Problem with Ryzen, threads and core dumps? (Steffen Graether)
>
>
> ----------------------------------------------------------------------
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> Message: 1
> Date: Tue, 8 Aug 2017 08:37:34 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] clayff forcefield
> Message-ID: <73598616-91d0-a438-e92c-278cd2ee9553 at vt.edu>
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> On 8/8/17 2:37 AM, G R wrote:
>
> >>    Hi,
> >>
> >       Thank you for your answer. yes, I know that I should make my own
> > forcefield in my working directory, and I made this forcefield, but when
> I
> > use x2top to generate itp file, gromacs could not find  my own forcefield
> > (I named the forcefield file clayff.ff) in my working directory. Gromacs
> > use the oplsaa in the share/top file instead, and obviusly the itp file
> > doesn't generate. So, I asked again to be sure about my procedure.
> >
> > In my last project I modified oplsaa for generating itp file for graphen
> > and I did not have this problem. Gromacs could easily recognize the
> > forcefiled file in current directory, but in clayff case I can't
> understand
> > why it read forcefield in shar/top instead of in current directory!
> >
> Probably because you're not selecting your force field properly.  gmx
> x2top has
> a -ff command-line argument, which defaults to OPLS-AA unless you specify
> otherwise.  You haven't provided your actual command yet, but I suspect
> that's
> you're problem.
>
> -Justin
>
> Thank you Justin. I used this command gmx x2top -f conf.gro -o sys.itp -ff
> clayff.ff. the error was ''couldn't find forcefield''. Then I used ''gmx
> x2top -f con.gro -o sys.itp -ff select'' for interactive selection, and I
> choosed clayff.ff. This time gromacs read the clayff forcefield in current
> directory. Is it right to use select? or I should do something else?
>

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