[gmx-users] LINCS warning: "Relative constraint deviation after LINCS"

[David]

On Tue, 2003-11-11 at 22:45, Martina Bertsch, PhD wrote:
> Thanks, David. The energies after SD-EM seem ok.
> 
> What do I do with the PR-MD and the LINCS warning? Please, see the
> GPCR_popc_pr.mdp below.

Hm, no obvious mistakes, you might want to remove the -DFLEX_SPC, and to
make a group of POPC+Protein for center-of-mass motion removal.

In which molecule do you get the lincs error? (print the rest of the
message, if it doesn't show try mdrun -v or even mdrun -v -debug).


> 
> > On Tue, 2003-11-11 at 21:07, Martina Bertsch, PhD wrote:
> > 
> > > Dear colleagues,
> > > 
> > > I use the final structure from my EM run as an input for the PR-MD. 
> > > My GPCR_popc_pr.mdp is attached below.
> > > 
> > > When I try running mdrun, I get a LINCS warning:
> > > 
> > >     "Relative constraint deviation after LINCS"
> > > 
> > > and the simulation stops at step 0.
> > > 
> > > How can I modify my *pr.mdp to remedy this?
> > > 
> > > Your advice is appreciated.
> > > 
> > > Best regards,
> > > 
> > > Martina Bertsch, Ph.D.
> > > Northwestern University
> > > Feinberg School of Medicine
> > > Molecular Pharmacology and Biological Chemistry
> > > 303 East Chicago Avenue
> > > Chicago, IL 60611
> > > 
> > > 
> > > ______________________________________________________________________
> > > 
> > > title               =  GPCR in POPC PR-MD
> > > cpp                 =  /lib/cpp
> > > define              =  -DFLEX_SPC
> > > define              =  -DPOSRES
> > > constraints         =  all-bonds
> > > constraint_algorithm = lincs
> > > integrator          =  md
> > > dt                  =  0.001    ; ps !
> > > ns
> > > teps              =  5000000 ; total 5 ns
> > > ;nstcomm             =  1
> > > nstxout             =  5000
> > > nstvout             =  5000
> > > nstfout             =  5000
> > > nstlog              =  5000
> > > nstenergy           =  5000
> > > nstxtcout           =  5000
> > > nstlist             =  10
> > > ns_type             =  grid
> > > rlist               =  1.0
> > > coulombtype         =  PME
> > > rcoulomb            =  1.0
> > > rvdw                =  1.2
> > > pbc                 =  xyz
> > > comm_mode           =  linear
> > > nstcomm             =  1
> > > fourierspacing      =  0.15
> > > pme_order           =  4
> > > optimize_fft        =  yes
> > > comm_grps           =  popc     sol
> > > ; Berendsen temperature coupling is on in two groups
> > > Tcoupl              =  berendsen
> > > tau_t               =  0.1      0.1     0.1
> > > tc-grps             =  protein  popc    sol
> > > ref_t               =  300      300     300
> > > ; Energy monitoring
> > > energygrps          =  protein  popc    sol
> > > ; Pressure coupling is on
> > > Pcoupl              =  berendsen
> > > pcoupltype          =  anisotropic
> > > tau_p               =  5        5       5       0       0       0
> > > compressibility     =  4.5e-5   4.5e-5  4.5e-5  0       0       0
> > > ref_p               =  1.0      1.0     1.0     0       0       0
> > > ; Generate velocites is on at 300 K.
> > > gen_vel             =  yes
> > > gen_temp            =  300.0
> > > gen_seed            =  280572
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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