[gmx-users] Variation of angles of simulation cell - regd
rameshgromacs at gmail.com
Mon Sep 10 05:52:25 CEST 2012
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. 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 ?.
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
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)
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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