[gmx-users] 256->1024 DPPC

Alberto.Imparato at na.infn.it Alberto.Imparato at na.infn.it
Wed Dec 3 16:05:01 CET 2003

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
~>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?

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