[gmx-users] Re: NPT and NVT simulations
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 28 01:07:33 CEST 2010
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
>>>>>> 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
>>>>
>>>>
>>>>
>>>> ========================================
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>> --
>> ========================================
>>
>>
>> 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
========================================
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