[gmx-users] Solvent density issue :
suru.vc at gmail.com
Thu Sep 29 14:22:58 CEST 2016
I am trying to solvate small organic molecule (8 molecules) of 20 atoms
each =160 atoms in Chloroform using Genbox.
according to the box volume that is created by the editconf (truncated
octahedron of 6nm) that is 166.28 nm, it should have roughly 1200 molecules
of chloroform. (not corrected for 160 atoms that are already present in the
after playing around with these numbers within two asterisks *
(CRYST1 *25.500 25.500 25.500* 90.00 90.00 90.00 P 1
1) in the
solvent PDB file, I reached to the right density, but the number of
molecules is way too much for the given volume.
can someone guide what is the correct way where I can have right density
and right amount of solvent molecules for the given sized box in the
I also tried to add the solvent molecules without solute in the box, but
the density and number correlation is still out of the order in that case.
REMARK THIS IS A SIMULATION BOX
CRYST1 *25.500 25.500 25.500* 90.00 90.00 90.00 P 1 1
ATOM 1 CL1 SOL 1 45.150 33.290 30.640 1.00 0.00
ATOM 2 C1 SOL 1 44.870 33.620 28.910 1.00 0.00
I will be grateful for any help in this direction.
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