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

[Nilesh Dhumal]

constraints = all-bonds is working. I have solvent molecule for which I
don't want constraints on them. I can't use constraints = all-bonds for
simulation.
Nilesh

On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote:
>

>
> 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
>>
>>
>>
>
> --
> ========================================
>
>
> 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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