[gmx-users] Bonds of chloroform molecules messed up after EM

Justin Lemkul 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.
Assistant Professor
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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