[gmx-users] gromos function type assigned by grompp
Romelia Salomon
romelia at caltech.edu
Fri Aug 8 01:38:37 CEST 2008
Ok, for my ligand I was using the Dundee PRODRG Server and the file
produced reads like this for example:
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.153 334720.0 0.153 334720.0 ; CAB CAE
2 3 1 0.139 418400.0 0.139 418400.0 ; CAE CAD
3 4 1 0.139 418400.0 0.139 418400.0 ; CAD CAC
4 5 1 0.153 334720.0 0.153 334720.0 ; CAC CAA
....
I was under the impression this site would be using GROMOS as the
forcefield, and actually the parameters do match the ones found in the
files share/top/ffgmx*.itp, would that be a bug from the website?
Thanks about your comments on what to keep in mind when using this
program, it'll save me some problems :)
Cheers,
Romelia
> 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/
>
> ========================================
> _______________________________________________
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--
****************************************
Romelia Salomon
Miller Group
316 Noyes
Chemistry Department
Caltech
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