[gmx-users] gromos function type assigned by grompp

Romelia Salomon romelia at caltech.edu
Fri Aug 8 02:00:22 CEST 2008 

Oh!! thanks!!... gromos, gromacs... that little x escaped my attention :)

That should solve all my doubts, thanks a lot!!

Romelia

>
>
> Romelia Salomon wrote:
>> 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?
>>
>
> No, there's no bug, you've just said it - the parameters come from ffgmx!
> The
> PRODRG server was originally for use with Gromos87-derived parameters.  If
> you're interested in using Gromos96 topologies (the 43a1 parameter set),
> you're
> better off using PRODRG2.5 at:
>
> http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta
>
> -Justin
>
>> 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
>>>>>>
>>>>>> ========================================
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>>>> Please search the archive at http://www.gromacs.org/search before
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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/
>>>
>>> ========================================
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>
>>
>>
>
> --
> ========================================
>
> 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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