[gmx-users] weird mdrun...using gromacs 3.3.3
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 8 19:59:54 CEST 2009
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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