Gaurav Chopra wrote:
Hi
I get the following error when using mdrun for a protein in solution.
I have checked the structure and everything looks fine to me. Could
you suggested anything else I could do.
Step -2, time -0.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.126305 (between atoms 892 and 894) rms 0.007000
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
898 899 41.6 0.1015 0.0997 0.1010
898 900 38.1 0.1038 0.0984 0.1010
starting mdrun 'HEADER Output set 125 with rmsf= .982 of
1nkd.cl_nH_tir.pdb in water'
100000 steps, 200.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 3.372058 (between atoms 894 and 895) rms 0.239340
bonds that rotated more than 30 degrees:
Thanks
gaurav
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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
Hi Gaurav,
what is your stepsize during the simulation? what is constrained? And
have you run a minimization before starting the simulation?
hear from you soon
Steffen
--
Dipl.-Chem. Steffen Wolf
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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
