[gmx-users] Re: NPT and NVT simulations
Justin A. Lemkul
jalemkul at vt.edu
Fri Jul 30 16:45:13 CEST 2010
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
>>>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ========================================
>>>>>>>> --
>>>>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ========================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>> --
>>>> ========================================
>>>>
>>>>
>>>>
>>>> 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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>>>>
>>>>
>>>>
>>>>
>>>
>>>
>> --
>> ========================================
>>
>>
>> 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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