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

[David]

On Tue, 2003-11-11 at 21:07, Martina Bertsch, PhD wrote:
> Dear colleagues,
> 
> I am simulating a GPC receptor embedded in a POPC membrane. According to 
> the protocol described in share/tutor/make_hole, I have generated the 
> protein accessible surface with GRASP, created a hole with a 1.2 nm 
> radius and run mdrun modified by Smith and Tieleman with hfm 25 and a 
> ndif
> p              =  0.001
> 
> After ~40 steps I get an error message:
> 
>     "Stepsize too small (... nm). Converged to machine precision, but 
> not to the requested precision (...)"
> 
> Searching the gmx archive, I find that this is because the SD algorithm 
> has problems and that the CG may give better results if you compile in 
> double precision.
> However, if the only aim is to start a MD simulation, then SD is good 
> enough and the final conformation from the EM can be used as an input 
> for MD.


this is in principle correct. do check your energies though, to see if
there are excessively large terms.

> 
> So, 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 !
> nsteps              =  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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