Alessandro Casoni wrote:
hi users,
I want to simulate a position restraint md.
pdb2gmx creates a correct protein.top and a posre.itp file.
but when I use " define = -DPOSRES" I have this error:
Step 1004, time 2.008 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.026978, max 1.366297 (between atoms 646 and 647)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
646 647 90.0 0.2562 0.2366 0.1000
and the simulation gives me a fatal error...
in my gro file atom 646 and 647 are:
65ASN N 646 8.608 5.187 2.517
65ASN H 647 8.510 5.206 2.518
please, give me some tips...
This has to be the most frequently-reported problem. Therefore, there are
thousands of posts in the list archive that may help. Also, from the wiki:
http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings
-Justin
Alessandro
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
