[gmx-users] Re: NPT and NVT simulations

Nilesh Dhumal ndhumal at andrew.cmu.edu
Wed Jul 28 14:44:49 CEST 2010


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.
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
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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
>>>
>>>
>>>
>>> ========================================
>>> --
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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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