[gmx-users] System instability with switched cut-off

[Matteus Lindgren]

Dear all

 

Im trying to extract the interaction energies between protein and solvent.
Since PME cant be used for this, plain cutoffs causes problems and shifted
cut-offs gives incorrect energies I want to use switched cutoff but with
rather long cutoffs to get the correct energy. 

 

Unfortunately my system is unstable and within a few ps the total energy and
kinetic energy fluctuates several hundred per cent. I´ve tried different
options but can´t get it to stabilize except if I´m using any other coulomb
type. Any ideas?

 

title                    = Dyna

cpp                      = /usr/bin/cpp

constraints              = hbonds

integrator               = md

dt                       = 0.002

nsteps                   = 20000000

nstxout                  = 20000000

nstvout                  = 20000000

nstfout                  = 5000

nstlog                   = 250

nstenergy                = 500

nstxtcout                = 500

xtc_grps                 = 

energygrps               = polar hydrophobic peptide  SOL 

nstlist                  = 1

ns_type                  = grid

coulombtype              = switch

rcoulomb_switch          = 1.4

rcoulomb                 = 1.7

rlist                    = 2.0

vdwtype                  = switch

rvdw_switch              = 1.4

rvdw                     = 1.7

tcoupl                   = nose-hoover

tc-grps                  = Protein    Non-Protein

tau_t                    = 0.5  0.5

ref_t                    = 298    298

Pcoupl                   = parrinello-rahman

tau_p                    = 1.0

compressibility          = 4.5e-5

ref_p                    = 1.0

 

;disre_fc                 = 30

 

gen_vel                  = yes

gen_temp                 = 298

gen_seed                 = 173529

unconstrained_start      = no

 

Thanks

Matteus 

 

--------------------------------------------------------- 

Matteus Lindgren, graduate student
Department of Chemistry, Umeå University 
SE-901 87 Umeå, Sweden
Phone:  +46 (0)90-7865368  

 

 

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