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On 11/06/2012 4:38 PM, rama david wrote:
<blockquote
cite="mid:CAD=-SYE+fZMRfc06T+d9JN3nAPUc0W75MCFeQOGvtNc-=qFHxw@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
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 moz-do-not-send="true"
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>
</blockquote>
<br>
That force is likely too large for comfort. Something is unhappy
such that you're seeing <a
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a>,
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.<br>
<br>
Mark<br>
<a
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up"></a>
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