[gmx-users] Variation of angles of simulation cell - regd
rameshgromacs at gmail.com
Mon Sep 10 08:35:41 CEST 2012
Thank you very much for your reply, I will change options
in .mdp file accordingly to get deformations in all possible
On Mon, Sep 10, 2012 at 9:41 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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
>> 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>
>>> 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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