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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