[gmx-users] Chloroform as Solvent

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 31 23:50:12 CEST 2010

Esteban Gabriel Vega Hissi wrote:
> Hi,
> I need to solvate a molecule with chloroform. Different from water and 
> DMSO, CHCL3 does not have a "solvent box" to use. I used the topology 
> present in ffG53a6.rtf and create a box and equilibrate it but when I 
> checked the trajectories some H atoms appear in an incorrect position, 
> i.e., behind the 3 chlorine away from carbon (to the opossite direction: 
> C-CL3-H) but  then I checked that the topology does not define any bond 
> between H and C.
> I rebuild the topology from scratch using the parameters present in this 
> FF. When I analyse the trajectories the geometry is OK, but the density 
> of the system is lower than expected for pure solvent. (In the previous 
> case when the geometry wasn't fine, the density of the system was OK).

Do you use constraints?  I once thought there should be a bond between C and H, 
but indeed there should not.  See my (erroneous) bug report here, particularly 
Berk's reply:


> Do you know what could be happening?

Without seeing your full .mdp file, no.

> Or do you have a a chloroform (all atoms) solvent box?

Your approach to creating one is more or less the right way to go.  There is an 
OPLS-AA CHCl3 box on the User Contributions section of the Gromacs site, but I 
have not personally used it, nor do I know if there is a literature reference to 
accompany it.


> Thanks in advance
> Esteban


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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