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

[Nilesh Dhumal]

Its oscillate between +/- 3-4 A.
If I freeze the distance by using freeze groups and dim in mdp file. It
works perfectly for NVT simulations. It oscillate for NPT simulation.
Nilesh

On Wed, August 4, 2010 9:56 pm, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> 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.
>
> So you used g_dist to determine the distances with the setup shown below,
> but did you correct for PBC effects?  Is there a systematic increase in
> the distance between the two particles, or does it oscillate?
>
> -Justin
>
>
>> 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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>>>
>>
>>
>>
>
> --
> ========================================
>
>
> 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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