mehmet kıytak wrote:
hi all...
ı have a problem.. ı got segmentation fault when run nvt equilibration..
ı use below mdp file
Please post a complete .mdp file. The Unix 'cat' command can be used to print
the contents of the text file, which can then be copied and pasted into an email.
couple-lambda0 = vdw ; only van der Waals interactions
couple-lambda1 = none ; turn off everything, in this case
only vdW
couple-intramol = no
nstdhdl = 10
It appears you are trying to do a free energy calculation by transforming your
system. Turn off the free energy code to determine whether or not this is a
source of the problem.
<snip>
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.337002, max 0.559171 (between atoms 1 and 4)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 90.0 0.1006 0.1091 0.1000
1 3 90.0 0.2058 0.1141 0.1000
1 4 90.0 0.3028 0.1559 0.1000
Back Off! I just backed up step3b_n3.pdb to ./#step3b_n3.pdb.1#
Back Off! I just backed up step3b_n4.pdb to ./#step3b_n4.pdb.1#
Back Off! I just backed up step3c_n2.pdb to ./#step3c_n2.pdb.1#
Back Off! I just backed up step3c_n3.pdb to ./#step3c_n3.pdb.1#
Back Off! I just backed up step3c_n4.pdb to ./#step3c_n4.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault
mkiytak@babil:~
PLEASE HELP ME...
LINCS warnings are the most common error reported to this list. Please refer to
the following pages for help:
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
If you still can't find your answer, refer to the list archive. As I said, such
errors are commonly reported. Surely you'll find something useful. The only
thing that can be said right now is that your system is unstable. Either you
need better minimization or equilibration (or both), your .mdp settings are
incorrect, or the free energy code is causing an instability (which is a symptom
of the first two points, it does not suggest the free energy code is not working).
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
