[gmx-users] System shrinkage during vacuum simulation

[David van der Spoel]

On 22/06/17 20:03, Sanim Rahman wrote:
> Hello everyone,
> 
> I ran a short MD simulation with a 3dc ewald geometry to simulate a vacuum
> slab at the top and bottom of my bilayer system. I equilibrated my system,
> tripled the size of my system in the z-direction and then added the 3dc
> geometry. My mdp script is written as below:
> 
turn off p coupling
> title = Production MD
> ; Run parameters
> integrator = md
> nsteps = 25000000
> dt    = 0.002
> 
> ; Output control
> nstxout = 2000
> nstvout = 2000
> nstxtcout = 2000
> nstenergy = 2000
> nstlog = 2000
> 
> ; Bond parameters
> continuation = yes
> constraint_algorithm = lincs
> constraints = all-bonds
> lincs_iter = 1
> lincs_order = 4
> 
> ; Neighborsearching
> ns_type = grid
> nstlist = 5
> rlist = 1.2
> rcoulomb = 1.6
> rvdw = 1.6
> 
> ; Electrostatics
> coulombtype = PME
> pme_order = 4
> fourierspacing = 0.16
> 
> ; Temperature coupling is on
> tcoupl = Nose-Hoover
> tc-grps = System
> tau_t = 0.2
> ref_t = 310
> 
> ; EWALD/PME/PPPM parameters =
> ewald-geometry: 3dc
> 
> ; Pressure coupling is on
> pcoupl = Parrinello-Rahman
> pcoupltype = semiisotropic
> tau_p = 2.0
> ref_p = 1.0   1.0
> compressibility = 4.5e-5 4.5e-5
> 
> ; Periodic boundary conditions
> pbc    = xyz
> 
> ; Dispersion correction
> DispCorr = EnerPres
> 
> ; Velocity generation
> gen_vel = no
> 
> My system shrunk down to a value close to the original dimension in the z
> direction as soon as the simulation started after I analyzed it using
> g_energy. Is there a mistake with my production .mdp file?
> 
> I will truly appreciate your assistance.
> 
> Regards,
> Sanim Rahman
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se