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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jun 20 19:48:54 CEST 2011


On 21/06/2011 2:10 AM, E. Nihal Korkmaz wrote:
> What would you suggest as a short time step? I was using 0.002 ps.

I'd suggest starting with maybe 100ps of 0.0005 ps time steps, but 
that's probably overkill.

> And just to make sure, would 5 ns of equilibration be enough for a 
> ~110 amino acid long protein?

I guess so. It's cheap.

Mark

> Thanks,
> Nihal
>
> On Mon, Jun 20, 2011 at 7:41 AM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     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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>
>
> -- 
> 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 <mailto:korkmaz at wisc.edu>
>
>

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