[gmx-users] 256->1024 DPPC

[David van der Spoel]

On Wed, 2003-12-03 at 16:03, Alberto.Imparato at na.infn.it 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:

do you have the correct topology? after genconf it should go
dppc 256
sol x
dppc 256
sol x
dppc 256
sol x
dppc 256
sol x

> 
> 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
> A.
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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