[gmx-users] gromos function type assigned by grompp

[Romelia Salomon]

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?

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