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

[Martina Bertsch, PhD]

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.

>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 !
>>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
>>

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