[gmx-users] LINCS warnings

[Mark Abraham]

On 11/06/2012 4:38 PM, rama david wrote:
> Hi Gromacs Friends ..
>
> I am trying to simulate octa-peptide in water model spc using G96 53a6 
> force field.
> my aim is to study the self assembly nature of these octapetide.
> I did following type of arrangment.
>
> I make antiparrallel arrangment of four peptide with distance of 0.5 
> nm in y direction,
> Then I translate these layer  in z direction, Such that separation in 
> each layer is 0.5 ,
>
> I arranged six layer in Z direction(total 24 peptide 6 * 4=24 ),
>
> I did Steepest Descent
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 100
>
> Double precision normally gives you higher accuracy.
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 108 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  = -9.2318734e+04
> Maximum force     =  6.8985820e+04 on atom 1359
> Norm of force     =  9.8921991e+02
>
>
> For nvt run I got Lincs Error
>
>
> Step 772, time 1.544 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.001014, max 0.009497 (between atoms 1360 and 1358)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    1359   1358   61.4    0.1000   0.1004      0.1000
>
> Step 773, time 1.546 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.003091, max 0.027499 (between atoms 1359 and 1358)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    1360   1358   32.1    0.0991   0.0985      0.1000
>    1359   1358   90.0    0.1004   0.1027      0.1000
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/mdlib/constr.c, 
> line: 176
>
> Fatal error:
> Too many LINCS warnings (1001)
> If you know what you are doing you can adjust the lincs warning 
> threshold in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "Carry Me Away" (Motors)
>
>
> When I check the website at http://www.gromacs.org/Documentation/Errors
>
> I come to know that system is unstable or not properly energy 
> minimised (e+04) is the source for such type of errors.
>
> But Truly I dont Want to change the arrangment (distance 0.5 nm),

That force is likely too large for comfort. Something is unhappy such 
that you're seeing 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up, and there 
are diagnostic strategies on that page. In particular, you must ensure 
you can simulate a single peptide successfully before you worry about 
doing more than one.

Mark
<http://www.gromacs.org/Documentation/Terminology/Blowing_Up>
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