[gmx-users] OPLS/AA + TIP5P, anybody?

[Christopher Neale]

Dear Grzegorz:

>From a quick look at your .mdp, I also suggest that you go back to your system including the peptide that you had managed to finish EM with modified flexible tip5p but then crashed with the standard rigid tip5p during MD and try the MD again using gen-vel = yes

if you're still seeing problems, why not upload your water-only system and your with-small-peptide test system to redmine. It's meant as a place to start a discussion, share files, and help us not to foget about a problem that may exist, so I am not sure why you hesitate.

Also, you said that the authors of that other OPLS-Tip5p paper had no problems. You might ask them for .gro .mdp and .top files so that you can see exactly what they did and how it differs from what you are doing.

Chris.

-- original message --

P.s. The mdp:

constraints         =  none
integrator          =  md
dt                  =  0.001    ; ps
nsteps              =  10000000     ; total 10 ns
nstcomm             =  1000
nstxout             =  0
nstvout             =  0
nstfout             =  0
nstxtcout           =  25
xtc_grps            =  System
nstlog              =  1000
nstenergy           =  1000
nstlist             =  20
ns_type             =  grid
rlist               =  1.3
coulombtype         =  PME
fourierspacing      =  0.1
pme_order           =  4
optimize_fft        =  yes
rcoulomb            =  1.3
rvdw                =  1.3
vdwtype             =  cut-off
pbc                 =  xyz
DispCorr            =  EnerPres
Tcoupl              =  v-rescale
ld_seed             =  -1
tc-grps             =  System
tau_t               =  0.1
ref_t               =  300.0
pcoupl              =  Parrinello-Rahman
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
gen_vel             =  no
cutoff-scheme       =  Verlet