[gmx-users] Inserting required no. of water using genbox -ci -nmol crashing
shivangi.nangia at gmail.com
Wed Jul 2 06:02:56 CEST 2014
This is regarding inserting required number of TIP3P water molecules using
I have a system containing POPC, peptide, water molecules & ions.
For some system set up, I had to delete all the waters and ions ( The box
size was not changed). Now I want to insert the same number of water
molecules back into the box (35228) but the job keeps crashing. When I run
it interactively it says there is not enough memory and if I submit in
queue the job just exits or goes into zombie mode.
System size: 9.38943 9.38943 15.54950
command: genbox_mpi -cp popc_pep.gro -ci spc.gro -nmol 35228 -o
I have tried varied kinds of spc.gro containing just one water molecule, 2
,3 and 4 (system size fixed accordingly using editconf -d 0 )
On using -cs option, lesser number of water molecules get inserted than
35228 on using the spc216.gro found in the /apps/gromacs/top folder.
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