Naga Rajesh Tummala wrote:
I usually use the final output file generated by GROMACS which contain
the velocity. But, I dont preserve the velocity every timestep.
CNT, CMT are constrained. I would want to make them move only in X
direction, but I cannot make the simulation work even when they are
constrained.
Unless you've specified constraints within the topology, you're not using
constraints:
; OPTIONS FOR BONDS
constraints = none
constraint-algorithm = lincs ; Type of constraint algorithm
unconstrained-start = no ; Do not constrain the start
configuration
Shake-SOR = no ; Use successive overrelaxation to
reduce the number of shake iterations
shake-tol = 1e-04 ; Relative tolerance of shake
lincs-order = 4 ; Highest order in the expansion
of the constraint coupling matrix
If you are using some constraints somewhere, try "unconstrained_start = yes"
instead.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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