[gmx-users] gromos function type assigned by grompp
romelia at caltech.edu
Fri Aug 8 01:19:55 CEST 2008
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
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 Salomon wrote:
>> 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
>> 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
> fine (bond type is 2). Furthermore, it's odd that grompp is including
> 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
> 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
> and may not be worth anything.
>> Is this right? Also, for clarification, I know Gromacs uses kj/mol and
>> as units, so does that mean that the values included in the ff*.itp
>> under the share/top/ directory are in those units?
> The units are all consistent.
>> Also I noticed that the .itp files for bonding interactions in
>> 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
>> things, thanks!!
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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