[gmx-users] Solvent density issue :
David van der Spoel
spoel at xray.bmc.uu.se
Thu Sep 29 14:33:17 CEST 2016
On 29/09/16 14:22, Surahit Chewle wrote:
> Dear Users,
> 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
You can just set gm solvate -maxsol N and then equilibrate your box.
> 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.
> TITLE chloroform
> REMARK THIS IS A SIMULATION BOX
> CRYST1 *25.500 25.500 25.500* 90.00 90.00 90.00 P 1 1
> MODEL 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.
> Surahit vc
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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