Hello All, It is a newbie question here, but I can not find a clear response. I would like to create a simple box of pure DECANE for MD with the Martini force field. I have tried do that with genbox (as for AA force field)
genbox_mpi -cp 1_CG_DECANE.pdb -ci 1_CG_DECANE.pdb -o CG_DECANE_box.gro -box 4.8 4.8 4.8 -nmol 255 -vdwd 0.21 where 1_CG_DECANE.pdb file contains three atoms (or beads) for decane. This atoms C1, C2 and C3 are placed according the geometry given in the martini_v2.0_solvents.itp file (i.e distance between beads of 4.7 A and angle of 180o). With this command, only the first atom of the DEC molecule is added in the box. So how to construct of pure solvent when i use the Martini force field In addition i have tried to use the martinize python script to transform a box of decane (AA) -> CG, but seemes to work only for proteins (correct ?). Thank you in advance for your help Stephane -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
