[gmx-users] Simulations in vacuo - energy increase

[Zoe Hall]

Gmx-users,



I am trying to carry out a simulation of lysozyme in vacuo using the OPLS-AA forcefield.  After energy minimisation, the protein is run for 10ps with position restraints and temperature coupling on. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using LINCS and a time step of 1fs. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used. When I carry out the 10ns simulation the total energy gradually increases, as does the temperature from 300 to 500K. I presume this is because the temperature coupling is turned off, however that is what I have noted from the literature that others do for their vacuum simulations. Can anyone shed any light on this? Following is my method.
integrator               = md
tinit                    = 0
dt                       = 0.001
nsteps                   = 10000000
nstxout                  = 20000
nstvout                  = 20000
nstfout                  = 0
nstlog                   = 100000
nstenergy                = 100000
nstxtcout                = 20000
energygrps               = Protein
nstcomm                 = 5
nstlist                  = 0
ns-type                  = simple
pbc                      = no
rlist                    = 0
coulombtype              = Cut-off
rcoulomb                 = 0
epsilon_r                = 2
vdw-type                 = Cut-off
rvdw                     =0
Tcoupl                   = no
tc-grps                  = Protein
tau_t                    = 0.1
ref_t                    = 300
Pcoupl                   = no
Pcoupltype               = Isotropic
tau_p                    = 1
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes ;
gen_temp                 =  300.0
gen_seed                 =  -1
constraints              = hbonds
constraint-algorithm     = LINCS
lincs_order              = 4

Thanks,

Zoe

Zoe Hall
Department of Chemistry
Oxford University

zoe.hall at chem.ox.ac.uk


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