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

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> 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.

I don't know if there have been any changes (I don't see anything in the 
revision history), but as far as I know, freezing is incompatible with NPT 
ensembles due to the inability to scale the frozen coordinates.

-Justin

> 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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> 
> 
> 

-- 
========================================

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

========================================