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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