[gmx-users] pr_md

[Luciane Vieira de Mello]

hi David,

> If you do EM do you have constraints turned off? (you should...)


that's what I have in em.mdp

; OPTIONS FOR BONDS     =
constraints              = none
; Type of constraint algorithm =
constraint-algorithm     = Lincs
; Do not constrain the start configuration =
unconstrained-start      = no
; Relative tolerance of shake =
shake-tol                = 1e-04
; Highest order in the expansion of the constraint coupling matrix =
lincs-order              = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle          = 30
; Convert harmonic bonds to morse potentials =
morse                    = no


is it all right?

thanks












>
> >Thanks in advance,
> >
> >Elza
> >Federal University of Rio de Janeiro
> >Biological Physics Lab
> >
> >> On Fri, 13 Dec 2002, Luciane Vieira de Mello wrote:
> >>
> >> >Dear all,
> >> >
> >> >I am running a pr_md, and got the following message:
> >> >
> >> This doesn't happen to be the CVS version of GROMACS?
> >>
> >> If not, did your minimization work out? Did energy converge reasonably
> >> well, are forces < 1000?
> >>
> >> >Step 17782, time 35.564 (ps)  LINCS WARNING
> >> >relative constraint deviation after LINCS:
> >> >max 21.626123 (between atoms 2688 and 2689) rms 0.471407
> >> >bonds that rotated more than 30 degrees:
> >> > atom 1 atom 2  angle  previous, current, constraint length
> >> >   2686   2687   51.8    0.1530   0.2187      0.1530
> >> >   2687   2688   89.8    0.1530   0.6611      0.1530
> >> >   2688   2689   89.8    0.1530   3.4618      0.1530
> >> >   2689   2690   89.8    0.1470   3.0238      0.1470
> >> >   2690   2691   87.9    0.1000   0.5723      0.1000
> >> >   2690   2692   87.3    0.1340   0.9661      0.1340
> >> >   2692   2693   60.8    0.1340   0.1681      0.1340
> >> >   2692   2696   61.8    0.1340   0.1693      0.1340
> >> >   2693   2694   50.5    0.1000   0.1501      0.1000
> >> >   2693   2695   54.8    0.1000   0.1592      0.1000
> >> >
> >> >in fact I got this message several times, involving different atoms.
> >> >
> >> >the atoms involved are part of the protein, which should be
> >> >constrain in the pr_md. Shouldn't they not be affected in this step?
> >> >
> >> >Has anyone got a message like this before? it is the first time I am
> >> >seeing it.
> >> >
> >> >cheers,
> >> >+-------------------------------------------------------------------------+
> >> >|                  Dra. Luciane Vieira de Mello Rigden
> >> |
> >> >| e-mail: mello at cenargen.embrapa.br
> >> |
> >> >| Embrapa Recursos Geneticos e Biotecnologia
> >> |
> >> >| Parque Estacao Biologica           |  http://www.cenargen.embrapa.br
> >> |
> >> >| PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741
> >> |
> >> >| 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658
> >> |
> >> >+-------------------------------------------------------------------------+
> >> >
> >> >
> >> >
> >> >
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