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

[Mark Abraham]

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
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists