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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