[gmx-users] Variation of angles of simulation cell - regd

ramesh cheerla rameshgromacs at gmail.com
Mon Sep 10 08:35:41 CEST 2012


Dear Mark,

             Thank you very much for your reply, I will change options
in .mdp file accordingly to get deformations in all possible
directions.

Thank you.

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 :-).
>
> 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 <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.
>>>
>>> Mark
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>
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