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 :-).
Mark
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)
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 = 0.12 ; 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 <[email protected]> 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.
Mark
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