[gmx-users] 1-4 interaction at distance larger than 1

houyi hzwwgy at hotmail.com
Mon Aug 3 16:06:41 CEST 2009

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

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