We are trying to increase the nsteps in mdp file, however it is not running properly. We want to increase the step number because we had the below error, when we analyze standar error:
--------------------------------------------------------------------------------------------------------
Read 1 sets of 4334 points, dt = 3
std. dev. relative deviation of
standard --------- cumulants from those of
set average deviation sqrt(n-1) a Gaussian distribition
cum. 3 cum. 4
SS1 6.621413e-01 7.053886e-03 1.071603e-04 -0.029 -0.043
Back Off! I just backed up errest.xvg to ./#errest.xvg.4#
Warning: tau2 is longer than the length of the data (12999)
the statistics might be bad
invalid fit: e.e. 0.0279777 a 0.853955 tau1 318.52 tau2 698399
Will fix tau2 at the total time: 12999
Using fixed parameters in curve fitting is temporarily not working.
Set 1: err.est. 0.00286789 a 0.95 tau1 447 tau2 12999
-------------------------------------------------------------------------------------------------
Additionally, we would like to know what "tau2" means and where can we identify this parameter in our .mdp file?
Thanks in advance for your response
I can solve it!! I do both, increase my steps of MD simulation and change the time to read, changing the flag -b (-1) First time to read from set, as below indicated
gmx analyze -f area-per-lipid.xvg -ee -b 12000
It was a convergence proble
:)
- Badges
- Science topic
- Similar topics
- Filing