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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jun 20 14:41:56 CEST 2011


On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote:
> 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.

The minimization is probably OK, but a period of equilibration at a 
short time step will probably help smooth the process out. Simulations 
in implicit solvent have few explicit degrees of freedom compared to 
explicit solvent, and might be rather more susceptible to equilibration 
issues if the generated velocities are randomly not-quite-good-enough.

Mark

> Thanks,
> Nihal
>
> On Sun, Jun 19, 2011 at 11:48 PM, E. Nihal Korkmaz 
> <enihalkorkmaz at gmail.com <mailto: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 <tel:608-265-3644>
>     Email: korkmaz at wisc.edu <mailto: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 <tel:608-265-3644>
> Email: korkmaz at wisc.edu <mailto:korkmaz at wisc.edu>
>
>

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