[gmx-users] Simulations in vacuo - energy increase

[David van der Spoel]

On 2011-04-30 14.17, Zoe Hall wrote:
> 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_
>
Are you sure h-bonds are being constrained, because otherwise the time 
step is too large? (maybe you need to write h-bonds). You may need to 
increase the constraint accuracy as well. We did all our vacuum calcs in 
double precision as well IIRC.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se