[gmx-users] Minimize energy of protein in CCl4

[Yang Li]

Hi!

I am trying to minimize two proteins in CCl4 solvent. When I do mdrun -v
-deffnm em, gromacs says too many LINCS warnings
I have tried the following:
1. use smaller time step
2. turn off temperature/pressure coupling
3. play around the lincs entries

Does this mean the minimization is just unachievable?
Below is the entries I used for bonds.

; OPTIONS FOR BONDS
constraints              = all-bonds
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Do not constrain the start configuration
continuation             = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR                = yes
; Relative tolerance of shake
shake-tol                = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter               = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle          = 40
; Convert harmonic bonds to morse potentials
morse                    = no


Thank you!