[gmx-users] Re: LINCS WARNING relative constraint deviation

[E. Nihal Korkmaz]

I also checked the output of the minimization:

Steepest Descents converged to machine precision in 402 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -1.81875038188621e+04
Maximum force     =  3.20769543152855e+02 on atom 331
Norm of force     =  2.04356801849931e+01

I assume the structure is not relaxed enough to start a simulation. How can
I get it minimize further? I increased the step size up to 0.1 ps, i still
get the same result.

Thanks,
Nihal

On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz
<enihalkorkmaz at gmail.com>wrote:

> Dear all,
>
> I am trying to simulate a GB simulation of a 112 amino acid long protein. I
> keep getting these errors,
>
> Step 27718, time 55.436 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 33.319842, max 438.763717 (between atoms 79 and 81)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>
> Step 27718, time 55.436 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.058237, max 1.390675 (between atoms 91 and 93)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>      91     92   50.2    0.1016   0.1065      0.1010
>      91     93   90.0    0.1002   0.2415      0.1010
>      91     94   70.2    0.1025   0.1066      0.1010
>      79     80   90.0    0.1057   1.0667      0.1090
>      79     81   90.0    1.3066  47.9342      0.1090
>      85     86   90.0    0.1084   0.1758      0.1090
>      85     87   90.0    1.0654   0.1668      0.1090
>      88     89   90.0    0.1097   0.6994      0.1090
>      88     90   90.0    0.1125   0.1097      0.1090
>      91     92   50.2    0.1016   0.1065      0.1010
>      91     93   90.0    0.1002   0.2415      0.1010
>      91     94   70.2    0.1025   0.1066      0.1010
>
>
> I am copying my mdp parameters below, I'd appreciate any suggestions to fix
> that.
>
> integrator               = sd
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 2500000
> simulation_part          = 1
> init_step                = 1
>
> nstxout                  = 5000
> nstvout                  = 5000
> nstenergy                = 500
> nstxtcout                = 500
> nstlog                   = 500
>
> xtc_grps                 = System
> energygrps               = System
> comm_mode                = Linear
> ; neighbor searching and vdw/pme setting up
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 2.0
>
> implicit_solvent         = GBSA
> gb_algorithm             = OBC
> gb_saltconc              = 0.15
> rgbradii                 = 2.0
>
> coulombtype              = Cut-off
> fourierspacing           = 0.1
> pme_order                = 6
> rcoulomb                 = 2.0
>
> vdwtype                  = Cut-off
> rvdw_switch              = 1.0
> rvdw                     = 2.0
>
> ; cpt control
> tcoupl                   = V-rescale
> tc-grps                  = System
> tau_t                    = 0.1
> ref_t                    = 300.0
>
> Pcoupl                   = Berendsen
> pcoupltype               = isotropic
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
>
> ; velocity & temperature control
> gen_vel                  = yes
> gen_temp                 = 300.0
> annealing                = no
> constraints              = hbonds
> constraint_algorithm     = lincs
> morse                    = no
>
>
> Thanks,
> --
> Elif Nihal Korkmaz
>
> Research Assistant
> University of Wisconsin - Biophysics
> Member of Qiang Cui & Thomas Record Labs
> 1101 University Ave, Rm. 8359
> Madison, WI 53706
> Phone:  608-265-3644
> Email:   korkmaz at wisc.edu
>
>
>


-- 
Elif Nihal Korkmaz

Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone:  608-265-3644
Email:   korkmaz at wisc.edu
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