houyi wrote:
Dear all,
I guess others have the same problem for me as well, and it may repeat
to ask it again due to i am new for gromacs- 3.3.3. my protein is
1z92.pdb. when i perform the energy minimization , i got this error. but
when i used for another small protein, which is 1ycr.pdb, it worked well
for all. i choose the OPLS-AA/L all-atom force field
my em.mdp is
title = protein
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 100
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
i found the website and some one said change the table extension to 2 or
3 or maybe more, it works for this step, but after performing the
postion constrains, it got the wrong results. so i guess i will not
change the table extension, and i do not why it only work for small
protein not for larger one, and i repeated sevel times, such as changing
timesteps and rlist and rcoulomb and rvdw to 0.9. still not working.
could anyone help me to explain this.
Your system is blowing up due to some non-physical interaction. Tweaking the
table-extension is probably not going to help. Some general references:
http://oldwiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off
http://oldwiki.gromacs.org/index.php/blowing_up
Without knowing more about how you prepared the system (exact commands), then
you will not likely get much more useful advice. Take a look at where things
are falling apart (atom numbers printed in the .log file) and see if you can
deduce the source of the problem.
-Justin
thank you very much
Reards,
Yi
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
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
========================================
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