[gmx-users] Bonds of chloroform molecules messed up after EM
jalemkul at vt.edu
Fri Oct 5 16:11:19 CEST 2018
On 10/5/18 10:07 AM, Lili Zhang wrote:
> Hi Justin,
> Thank you for your reply.
> Yes, this is the chloroform based on DH model. The chlo.str file was kindly
> shared with me by Dr. MacKerell. I noticed two bond force constant kb and angle
> force constant ktheta are zero, in the str file.
> CCM CLCM 500.0 1.758
> CCM HCM 500.0 1.100
> CLCM CLCM 0.0 2.9028314
> HCM CLCM 0.0 2.3383924
> CLCM CCM CLCM 0.0 111.30
> HCM CCM CLCM 0.0 107.57
> I converted the force constant kb in the first two rows from kcal/mole/A**2
> (CHARMM unit) to kJ/mole/nm**2 (Gromacs unit), so I did not assign
> arbitrary values.
Note the following from that topology:
BOND CL1 CL2 CL1 CL3 !for shake
BOND CL1 HX CL2 HX CL3 HX ! for shake
These "non-chemical" bonds imply that the distances between all atoms
are supposed to be rigid, rendering the rest of the bonded parameters
fairly irrelevant. You can't allow the angle force constants to simply
be zero and ignore the requirements of these constraints. You can try to
implement a fully rigid model in GROMACS, but as I recall from working
with chloroform (with a different force field) several years ago,
GROMACS wouldn't allow for a molecule to have more constraints than
degrees of freedom. You may have to use different software that is more
suited for simulating rigid species.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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