Dear Gromacs-Users,
we have the following problem: after running several hundred nanoseconds
of a peptide (Gromos FF 53a6) in spc-water (NpT ensemble), we recognized
that the tolerance of shake (all-bonds were constrained) was wrongly
adjusted: instead of calculating with shake_tol = 0.0001, the value was
0.01. Our question is now if the additional noise we produced in this
way makes a repetition of the runs necessary or not? Density, pressure,
etc. of the boxes are ok, but we are not sure what kind of artifacts
could have arisen due to this wrong setup. The integration time step was
2 fs.
Thanks for your help and suggestions!
Cheers,
Andreas
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
