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:
http://bugzilla.gromacs.org/show_bug.cgi?id=359
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.
-Justin
Thanks in advance
Esteban
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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