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

[Justin A. Lemkul]

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

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