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.
thank you very much
Reards,
Yi
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