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