[gmx-users] Solvent density issue :

[David van der Spoel]

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
> system)
>
> 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
> system?

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.
>
> best,
> 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