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

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 5 04:44:42 CEST 2010



Nilesh Dhumal wrote:
> Then it looks there is bug ater define the constraints in itp file, bond
> distance changes.
> 
> 

Then file a bugzilla so the developers can either confirm the bug and fix it, or 
provide an explanation as to what is going on.

-Justin

> 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
>>>>
>>>>
>>>>
>>>> ========================================
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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

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



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