[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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>>>> 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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>>
>
>
>
--
========================================
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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