[gmx-users] Chloroform as Solvent
Esteban Gabriel Vega Hissi
egvega at gmail.com
Wed Mar 31 23:38:22 CEST 2010
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 know what could be happening?
Or do you have a a chloroform (all atoms) solvent box?
Thanks in advance
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