[gmx-users] Re: NPT and NVT simulations
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Fri Jul 30 16:54:15 CEST 2010
I am going to put solvent arond this solute. I want to freeze the distance
only for solute not for solvent.
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?
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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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
>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>>> Please search the archive at http://www.gromacs.org/search
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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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ========================================
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at http://www.gromacs.org/search before
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>>>>> Can't
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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
>
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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