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

Nilesh Dhumal ndhumal at andrew.cmu.edu
Thu Aug 5 04:39:03 CEST 2010 

Then it looks there is bug ater define the constraints in itp file, bond
distance changes.


On Wed, August 4, 2010 10:22 pm, Justin A. Lemkul wrote:
>

>
> 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
>>>
>>>
>>>
>>> ========================================
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
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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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