[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         = 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" 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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