[gmx-users] LINCS warning: "Relative constraint deviation after LINCS"
spoel at xray.bmc.uu.se
Tue Nov 11 21:50:01 CET 2003
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
> 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 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
More information about the gromacs.org_gmx-users