[gmx-users] Re: NPT and NVT simulations

[Nilesh Dhumal]

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


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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ========================================
>>>>> --
>>>>> 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
>>>
>>>
>>>
>>> ========================================
>>>
>>>
>>>
>>>
>>
>>
>>
>
> --
> ========================================
>
>
> 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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