[gmx-users] LINCS warnings

[rama david]

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),

Please Help me to solve the above problem,

All suggestion are welcome



With Best Wishes,
Rama David
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