[gmx-users] RE: How can I generate a Input *.gro file of coarse grain(xuji)

xuji xuji at home.ipe.ac.cn
Wed Oct 22 09:40:36 CEST 2008

Hi Yang:
I checked the potential fnctions the Martini force field used in Gromacs. 
The bond and angle potential funtions are g96 harmonic potential functions.
The VDW and COULOMB potential functions are in nb_kernel330_x86_64_sse.s file 
in my workstation's environment.

>Hi ,
>I was also engaged in dealing with the problem about the course grain model . I find that in this CG force field , the potential functions almost don't correspond to that in the gromacs.
>Hence, I wonder whether you know to how to define these new potential functions.
>Thank you in advance.

And Hi all gromacs users:
These two days, I choose one CG molecule of DPPC of the exmple "Solvated DPPC and POPE vesicles"
in http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html. And I translate the DPPC meloclue to fill
the box as three dimensional arrays. And then I fill the system with CG waters. In this method the 
whole system is absolutely not equilibrium. And I always get "segment fault" when I run this system 
with GROMACS 4.0.
And I also try to simulate this type of system with "GROMACS 3.3.3", but I get 

Program grompp, VERSION 3.3.3
Source code file: grompp.c, line: 469
Fatal error:
number of coordinates in coordinate file (dppc_vesicle.gro, 72076)
             does not match topology (dppc_vesicle.top, 0)

when I use grompp to generate the input file of mdrun.
How can I solve these two problems?
Appreciate any help in advance!

        xuji at home.ipe.ac.cn

More information about the gromacs.org_gmx-users mailing list