manjula kasinathan wrote:
Hi all
i have done protein protein interaction and the complex structure
was taken for MD simulation using Gromacs. the length of the protein was
around 1100 aa. while performing mdrun step for position restrain i got
error. i have carried out mdrun for 1ps and the command given for mdrun
and position restrain are
grompp -f *.pdb -c *.gro -p top.top -o *.tpr
mdrun -v -deffnm pr
error i got was
starting mdrun '? in water'
500 steps, 1.0 ps.
step 400, remaining runtime: 133 s
Step 416, time 0.832 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000577, max 0.008379 (between atoms 5530 and 5532)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
8190 8191 30.7 0.1014 0.1000 0.1000
Step 419, time 0.838 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000874, max 0.019432 (between atoms 5526 and 5527)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
112 113 31.0 0.1017 0.1002 0.1000
Step 430, time 0.86 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 158552932798158.562500, max 14888250728513536.000000 (between atoms
1734 and 1735)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4469 4471 66.7 0.1327 0.5535 0.1330
4469 4470 69.6 0.1227 0.5336 0.1230
8001 8003 47.0 0.0999 0.0998 0.1000
7995 7996 30.0 0.1001 0.0999 0.1000
7970 7971 34.0 0.0999 0.1002 0.1000
t = 0.860 ps: Water molecule starting at atom 81142 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
could any one pls help me to overcome this problem.how give me some ideas.
looking forward for a solution. thanx in advance.
Please consult the following:
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
...as well as searching for this error in the mailing list archive. You will
find thousands of posts, doubtless some of them will provide you with some
information.
If you want specific help, please post (at the very least) your .mdp file and
describe any steps you have taken to construct and/or energy-minimize your
structure.
-Justin
--
With Regards,
Manjulakasinathan
--
========================================
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
========================================
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