[gmx-users] Re: NPT and NVT simulations

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 27 18:38:34 CEST 2010



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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