[gmx-users] frezzing a bond : NPT and NVT simulations

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello
> I am trying to constraints of a bond. I checked the distance using g_dist,
> distance changes from 3.5 A to ~ 8.0A.
> Can anyone tell why it changes.
> Here I have pasted mdp file and itp file.

Maybe there's a bug in the interpretation of the constraints?  The combination 
of "constraints = none" + [constraints] directive should constrain the bond. 
Have you tried simply defining a [bonds] directive and using "constraints = 
all-bonds"?

-Justin

> Nilesh
> Solvent.itp
> ; Derived from parsing of runfiles/alat.top.orig
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> ;1               3               yes             0.5     0.5
> ; comb-rule 3 is square-root sigma, the OPLSAA version
> 
> [ atomtypes ]
> ; full atom descriptions are available in ffoplsaa.atp
> ;  name  bond_type    mass    charge   ptype          sigma      epsilon
>   opls_997   PA 0   100.0000    1.000       A    0.40000e-01  0.82890e-01
>   opls_998   NE 0   100.0000   -1.000       A    0.40000e-01  0.82890e-01
> 
> [ bondtypes ]
> ; i    j  func       b0          kb
>   PA    NE      1    0.350000   000000
> 
> [ moleculetype ]
>  ; name  nrexcl
>  ABC         3
> 
> [ atoms ]
>  ;   nr  type    resnr   residu  atom    cgnr    charge mass
>  1  opls_997        1       ABC    PA      1        1.0000  100.0000
>  2  opls_998        1       ABC    NE      1       -1.0000  100.000
> 
> [ constraints ]
>   1   2   1    0.35000
> 
> 
> pr.mdp
> title               =  cpeptid position restraining
> cpp                 =  /usr/bin/cpp
> constraints         =  none
> integrator          =  md
> dt                  =  0.001    ; ps !
> nsteps              =  250000      ; total 1.0 ps.
> nstcomm             =  1
> nstxout             =  10
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> coulombtype         = PME
> vdwtype             = cut-off
> rcoulomb            =  1.0
> rvdw                =  1.4
> fourierspacing      = 0.12
> fourier_nx               = 0
> fourier_ny               = 0
> fourier_nz               = 0
> pme_order           = 4
> ewald_rtol          = 1e-5
> optimize_fft        = yes
> constraint-algorithm     = SHAKE
> ; Berendsen temperature coupling is on
> Tcoupl = v-rescale
> tau_t = 0.1
> tc-grps  =system
> ref_t =   400
> ; Pressure coupling is not  on
> Pcoupl              = no
> pcoupltype          = isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  400.0
> gen_seed            =  173529
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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