[gmx-users] Variation of angles of simulation cell - regd
Mark.Abraham at anu.edu.au
Mon Sep 10 06:11:18 CEST 2012
On 10/09/2012 1:52 PM, ramesh cheerla wrote:
> Dear Mark,
> Thank you very much for your reply and valuable
> suggestions, I have used compressibility values as "compressibility
> = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0" in my .mdp file.
So you're getting the (lack of) box deformations you're asking for with
these zero compressibilities. Having non-zero off-diagonal
compressibilities with ref_p sounds like a disaster, too.
> Actually I
> am interested in melting simulations of a polymer crystal, but I
> haven't found any compressibility values for my system in literature,
> So that I have used compressibility values of water in my simulations,
> Can I do like this ?.
Maybe. You need to do some literature work, not ask some semi-random
people on the internet :-).
> Following is the my .mdp file used for production, can you please go
> through the .mdp file and suggest me if any modifications are required
> to get correct lattice parameters.
> title = CHARMM 27 MD
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 500000 ; 2 * 500000 = 1000 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)
> 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
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.12 ; 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 = 20 ; reference temperature, one for each
> group, in K
> ; Pressure coupling is on
> pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
> pcoupltype = anisotropic ; non uniform scaling of box vectors
> tau_p = 2.0 ; time constant, in ps
> ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 ;
> reference pressure, in bar
> compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0 ;
> 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
> Thank you in advance.
> On Sun, Sep 9, 2012 at 9:17 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>> On 9/09/2012 11:41 PM, ramesh cheerla wrote:
>>> Dear Gromacs users,
>>> Recently I have converted each frame of the
>>> trajectory to a pdb file using gromacs tool "g_trjconv" and then
>>> have extracted angles from the CRYST1 record of pdb file, to see how
>>> they are varying in simulation. By doing so I have observed that my
>>> box angles alpha and gamma are not at all varying through out the
>>> simulation these values are remains at "90" degrees and there is a
>>> change in beta value.
>>> I have used "triclinic box" for simulations of my system with angles
>>> alpha = 90, beta=120 and gamma=90 and have used "NPT" ensemble with
>>> following options in mdp file "pcoupltype = anisotropic and
>>> ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 "
>>> here my questions are:
>>> 1) What might be the probable reason for constant values of alpha and
>>> beta ( why these values are not changing).
>> See 7.3.15, which of course you read before using anisotropic coupling.
>> You're making life hard by not giving your full .mdp file, because you're
>> leaving us to guess about your compressibilities. Do summarise, but don't
>> exclude. :-) Presumably your choices are consistent with a monoclinic box
>> staying that way.
>>> 2) Am I following correct protocol to extract angles, or Is there any
>>> better way to extract angles from trajectory.
>> If you want lattice parameters, that's probably the best way to get them.
>>> 3) Am I using correct options in .mdp file.
>> Can't tell.
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