[gmx-users] gromos function type assigned by grompp

[Justin A. Lemkul]

Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

> Quoting Romelia Salomon <romelia at caltech.edu>:
>
> > Hi Justin
> >
> > thanks for your email, yes I used the -pp option to print out the file I
> > showed here. I am using gromacs-3.3.3 and I compiled it just doing the
> > typical ./configure make make install and I checked and it's using cc as a
> > compiler.
> >
> >
> > What I was trying to do is to run a calculation using Gromos forcefield in
> > another program I have and I was trying to debug it by trying to match the
> > energy coming from gromacs using that same forcefield. I tried the -pp
> > option in grompp to show explicitly the parameters being used during the
> > calculation and that is how I got the file I showed. I tried the gmxdump
> > and that seems to be ok. I wrote my conversion file based on that file so
> > now it works fine :).
> >
> > Just one last question, in the PRODRG website the gromacs topology files
> > generated have function 1 for both angles and bonds, that means that the
> > functions to be used are the regular harmonic form for both, right?
> >
>
> Yes, if you're using the ffgmx force field.  Beware of doing so!  The manual,
> the listing in pdb2gmx, and countless posts on this list warn that ffgmx is
> old
> and deprecated.  If you are indeed trying to use a Gromos96 parameter set, be
> sure you're calling the right force field!
>
> Also note that PRODRG topologies often require refinement of (at the very
> least)
> charges and charge groups.  Just something to keep in mind.
>
> -Justin
>
> > Thanks a lot for your time!!!
> >
> > Romelia
> >
> >
> > >
> > >
> > > Romelia Salomon wrote:
> > >> Hi
> > >>
> > >> I am trying to set a calculation based on the GROMOS force field in a
> > >> program I have and I am using GROMACS to generate the (starting) input
> > >> files for me. From reading the manual I know that GROMOS uses a fourth
> > >> power potential (type 2) for bonds and a cosine based angle potential
> > >> (type 2), but I noticed that when using grompp to include the values for
> > >> the parameters explicitly it changes the type from 2 to 1, for example:
> > >>
> > >> topology file before grompp
> > >> [ bonds ]
> > >> ;  ai    aj funct            c0            c1            c2
> > >> c3
> > >>     1     2     2    gb_2
> > >>     1     3     2    gb_2
> > >>     1     4     2    gb_2
> > >>     1     5     2    gb_20
> > >>     5     6     2    gb_26
> > >>     5    10     2    gb_26
> > >> after using grompp
> > >
> > > This would be from the -pp flag of grompp?
> > >
> > >> [ bonds ]
> > >> ;  ai    aj  tp parameters
> > >>     N    H1   1       0.1 1.87e+07
> > >>     N    H2   1       0.1 1.87e+07
> > >>     N    H3   1       0.1 1.87e+07
> > >>     N    CA   1     0.147 8.71e+06
> > >>    CA    CB   1     0.153 7.15e+06
> > >>    CA     C   1     0.153 7.15e+06
> > >>
> > >
> > > Which version of Gromacs are you using?  I'm using 3.3.3, and mine works
> > > just
> > > fine (bond type is 2).  Furthermore, it's odd that grompp is including
> > > atom
> > > names instead of numbers...unless you've interpreted what the output
> > > really is
> > > and transcribed it differently :)
> > >
> > > If grompp is changing these, then perhaps it's a bug.  Note that weird
> > > behavior
> > > arises when Gromacs is compiled with gcc 4.1.x, as has been beaten to
> > > death on
> > > this list :)  Without knowing more about your system, this is pure
> > > speculation
> > > and may not be worth anything.
> > >
> > >> Is this right? Also, for clarification, I know Gromacs uses kj/mol and
> > >> nm
> > >> as units, so does that mean that the values included in the ff*.itp
> > >> files
> > >> under the share/top/ directory are in those units?
> > >>
> > >
> > > The units are all consistent.
> > >
> > > -Justin
> > >
> > >> Also I noticed that the .itp files for bonding interactions in
> > >> gmxbon.itp
> > >> have declared a type 1 function which would be the regular harmonic one.
> > >>
> > >> Sorry for the very basic questions, but I wanted to be certain about
> > >> this
> > >> things, thanks!!
> > >>
> > >> Romelia
> > >>
> > >> Thanks!
> > >>
> > >>
> > >
> > > --
> > > ========================================
> > >
> > > Justin A. Lemkul
> > > Graduate Research Assistant
> > > 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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> >
> >
> > --
> > ****************************************
> > Romelia Salomon
> > Miller Group
> > 316 Noyes
> > Chemistry Department
> > Caltech
> >
> >
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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