[gmx-users] 256->1024 DPPC

[Marcos Villarreal]

On Wednesday 03 December 2003 12:03, you wrote:
> Hi
> I want to run a 1024 DPPC +water simulation, starting from
> the output of a previous simulation with 256DPPC + water.
> A while ago, some of you wrote me to use something like
> ~>genconf  -nbox 2 2 1 -f 256.gro -o 1024.gro
> but the program crashes aftet the step 0, this is the typical
> error output:
>
> Step -2, time -0.004 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 403.568115 (between atoms 50954 and 50955) rms 18.080801
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   30451  30454  174.8    5.3362   1.2299      0.1470
>   30452  30454  172.9    5.1807   1.2427      0.1470
>   .......
>   .......
>
> If eliminate by hand the SOL molecules from 256.gro ---> 256-withoutSOL.gro
> then
> ~>genconf  -nbox 2 2 1 -f 256-withoutSOL.gro -o 1024-withoutSOL.gro
> and then randomy add SOLs with genbox
> genbox -cp 1024-withoutSOL.gro -cs -o 1024.gro
> the program works
> but I find out SOL molecules in the center of the bilayer, which is
> a bit annoying,
>
> Can somebody help?
> Thanks

It seems a problem in the order of the atoms in the 1024.gro file
you can reorder the file with something like this:

grep DPP     1024.gro > a
grep SOL     1024.gro > b
cat a b > 1204reorder.gro

then you have to add the first (num of atoms) and the last (cell dim) lines 
of 1024.gro to 1024reorder.gro

Saludos,
		Marcos.

-- 
Marcos Villarreal
Grupo de Biofisica
Departamento de Quimica Biologica - CIQUIBIC.
Universidad Nacional de Cordoba.
Cordoba. Argentina.
http://www.fcq.unc.edu.ar/ciquibic