[gmx-users] Re: NPT and NVT simulations

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 30 16:58:32 CEST 2010 


Nilesh Dhumal wrote:
> I am going to put solvent arond this solute. I want to freeze the distance
> only for solute not for solvent.

Then the approach I described will work fine.  Either constrain all bonds or use 
a distance restraint.

-Justin

> Nilesl
> 
> On Fri, July 30, 2010 10:45 am, Justin A. Lemkul wrote:
> 
>> Nilesh Dhumal wrote:
>>
>>> I put the constraints on PA-NE to keep the bond length 3.5 A.
>>> After calculating the g_dist I noted that the  bond length is atound 5.5
>>>  A. Can you tell why its taking 5.5 A.
>>> If I difine contraints=all-bonds in mdp file then it shows 3.5 A proper
>>> bond length.
>> From your original post some time ago, it was not clear that you only had
>> one bond to deal with.  If this is the case, then your approach sounds
>> fine, just use a normal [ bonds ] directive and set "constraints =
>> all-bonds."  As you say, that works, so I don't see what the problem is.
>> Are you going to be developing
>> a more complex system for which you don't want other bonds constrained,
>> just the one defined below?  Another approach would be a distance
>> restraint, but I don't believe that will absolutely fix the distance,
>> unless your tolerance is set very strictly.
>>
>> -Justin
>>
>>
>>> Can u tell where is the problem.
>>> Here I pasted the .itp file
>>>
>>>
>>> ; 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         2
>>>
>>>
>>> [ 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 ]
>>> ; i    j  func       b0          kb
>>> 1    2      1    0.350000
>>>
>>>
>>>
>>> On Tue, July 27, 2010 7:07 pm, Justin A. Lemkul wrote:
>>>
>>>
>>>> Nilesh Dhumal wrote:
>>>>
>>>>
>>>>> Can you tell where I am going worng. Here I pasted my .itp file
>>>>>
>>>>>
>>>>>
>>>>> ; 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
>>>>>
>>>>>
>>>>> [ constraints ]
>>>>> ; i    j  func       b0          kb
>>>>> 1    2      1    0.350000
>>>>>
>>>>>
>>>>>
>>>>>
>>>> As I said before (and is explained in the manual), [constraints],
>>>> like any other bonded parameter, must belong to a [moleculetype],
>>>> which you have not defined here.  You've got atom types and force
>>>> field information, but no molecule to which the constraints are
>>>> applied.
>>>>
>>>> -Justin
>>>>
>>>>
>>>>
>>>>> Nilesh
>>>>>
>>>>>
>>>>>
>>>>> On Tue, July 27, 2010 12:38 pm, Justin A. Lemkul wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Nilesh Dhumal wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> still I am getting the same error.
>>>>>>>
>>>>>>> Now I added this two lines
>>>>>>> [ constraints ]
>>>>>>> 1   2   1    0.350000
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> Then you still have the directive in the wrong place.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> On Tue, July 27, 2010 12:34 pm, Justin A. Lemkul wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> Nilesh Dhumal wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> I am using opls force field. I have solvent.itp file.
>>>>>>>>> I added follwing line in my solvent.itp file.
>>>>>>>>> [ constraints ]
>>>>>>>>> opls_997  opls_998   1    0.350000 I am getting the
>>>>>>>>> following error
>>>>>>>>>
>>>>>>>>>
>>>>>>>> You don't define constraints with atom types, you use atom
>>>>>>>> numbers. See the manual.
>>>>>>>>
>>>>>>>>> Fatal error:
>>>>>>>>> Syntax error - File solvent.itp, line 13
>>>>>>>>> Last line read:
>>>>>>>>> ' [ constraints ]'
>>>>>>>>> Invalid order for directive constraints
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> Then you've put it in the wrong place.  Like any other bonded
>>>>>>>>  term, [constraints] belongs to the moleculetype to which the
>>>>>>>>  constraint is to be applied.
>>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Nilesh
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, July 27, 2010 11:29 am, Justin A. Lemkul wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Yes, if you define it in a [ constraints ] directive, and
>>>>>>>>>> use "constraints =
>>>>>>>>>> none" in your .mdp file, so that other bonds will not be
>>>>>>>>>> converted to constraints, but the one you explicitly set
>>>>>>>>>> in the topology will be used.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> -Justin
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Nilesh Dhumal wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Can I put constraint on selected bond?
>>>>>>>>>>> Nilesh
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Sun, July 25, 2010 11:33 pm, Vitaly Chaban wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> 1. Using freezegrps is not generally a good idea to
>>>>>>>>>>>> fix a bond length. Look at the constraints mechenism
>>>>>>>>>>>> better. Or just
>>>>>>>>>>>> try a bigger force constant in topology.
>>>>>>>>>>>>
>>>>>>>>>>>> 2. NPT and freezegrps do not interact correctly,
>>>>>>>>>>>> since freezegrps just freezes any changes of atom
>>>>>>>>>>>> positions, so they are not rescaled even if the box
>>>>>>>>>>>> size is changed in NPT.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> 3. Anyway, I think you have defined incorrect groups
>>>>>>>>>>>> if your atoms of interest are still movable. Check a
>>>>>>>>>>>> diffusion constant of your bonded atoms, it should be
>>>>>>>>>>>> zero in the case of freezegrps.
>>>>>>>>>>>>
>>>>>>>>>>>> Dr. Vitaly Chaban
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> I am trying to freeze a bond (3.5 A) in my system.
>>>>>>>>>>>>> I
>>>>>>>>>>>>> used the index file to define group and I added this
>>>>>>>>>>>>> two lines in my .mdp file.
>>>>>>>>>>>>>
>>>>>>>>>>>>> freezegrps         = PA NE freezedim   = Y Y Y Y Y
>>>>>>>>>>>>> Y
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> I used g_dist to verify the distance between the
>>>>>>>>>>>>> freezing atoms. During the NVT simulation the
>>>>>>>>>>>>> distace is around 3.449 A and its constant though out
>>>>>>>>>>>>> the simulation. For NPT simulation the distance
>>>>>>>>>>>>> varies from 3.449 to 3.1. Can you tell why distance
>>>>>>>>>>>>> changes in NPT not in NVT. How can I freeze a bond
>>>>>>>>>>>>> om NPT simulation?
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>> --
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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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ========================================
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>> --
>>>>>> ========================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> 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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