[gmx-users] simulation single molecule in water

[Dr. Vitaly Chaban]

Your problem has nothing to do with barostat.

There is such thing as DispCorr. I am unsure whether if should be turned on
or off in case of your model. It does influence density to certain extent.


Dr. Vitaly Chaban







> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Souilem Safa
> Sent: Tuesday, 7 May 2013 4:38 PM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] simulation single molecule in water
>
> Dear gromacs users,
> I'm simulating a single molecule in spc water. I'm using a cubic water box
> which has 3.4 nm size.
> I got the toplogy of my molecule via PRODRG.
> After running minimization, NVT , NPT and MD for 10 ns , I checked the
> density of water ,it was less than the real value (1000 kg m\S-3\N)
> ,actually I got around 950.
> I have checked my mdp file in the NPT step and I was wondering about tau_p
> that I should use. First I used 2.0 ps with Parrinello-Rahman coupling.
> After checking in gromacs archive, I found it is better to use 0.5 ps, I
> have changed tau-p ,but I still have density value less than 1000.
> Details of my  mdp file are below :
>  Run parameters
> integrator    = md        ; leap-frog integrator
> nsteps        = 5000000    ; 2 * 5000000 = 10000 ps, 1 ns
> dt        = 0.002        ; 2 fs
> ; Output control
> nstxout        = 1000        ; save coordinates every 2 ps
> nstvout        = 1000        ; save velocities every 2 ps
> nstxtcout    = 1000        ; xtc compressed trajectory output every 2 ps
> nstenergy    = 1000        ; save energies every 2 ps
> nstlog        = 1000        ; update log file every 2 ps
> ; Bond parameters
> continuation    = yes        ; Restarting after NPT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints    = all-bonds    ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter    = 1        ; accuracy of LINCS
> lincs_order    = 4        ; also related to accuracy
> ; Neighborsearching
> ns_type        = grid        ; search neighboring grid cells
> nstlist        = 5        ; 10 fs
> rlist        = 1.0        ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 1.0        ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.0        ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype    = PME        ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order    = 4        ; cubic interpolation
> fourierspacing    = 0.16        ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl        = V-rescale    ; modified Berendsen thermostat
> tc-grps        = system    ; two coupling groups - more accurate
> tau_t        = 0.1        ; time constant, in ps
> ref_t        = 300         ; reference temperature, one for each group, in
> K
> ; Pressure coupling is on
> pcoupl        = Parrinello-Rahman    ; Pressure coupling on in NPT
> pcoupltype    = isotropic    ; uniform scaling of box vectors
> tau_p        = 0.50        ; time constant, in ps
> ref_p        = 1.0        ; reference pressure, in bar
> compressibility = 4.5e-5    ; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc        = xyz        ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel        = no        ; Velocity generation is off
>
> What should be the origin of this density difference?
> looking forward to your advise
> --
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