[gmx-users] inquiring for solving trjconv problems
Mehdi Bagherpour
mbagherpour7749 at gmail.com
Mon Jan 21 02:34:57 CET 2013
excuse me Dear Justin
I could not understand exactly what to do?
My simulation system is DNA in water.
when I use from bellow command I choose DNA group.
In 25000 snapshot approximately in 1000 of this structures two strands of
DNA are separated.
*
trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center*
Will write pdb: Protein data bank file
Reading file md6.tpr, VERSION 4.5.5 (single precision)
Reading file md6.tpr, VERSION 4.5.5 (single precision)
Select group for centering
Group 0 ( System) has 35194 elements
* Group 1 ( DNA) has 1012 elements*
Group 2 ( MG) has 4 elements
Group 3 ( CL) has 29 elements
Group 4 ( K) has 51 elements
Group 5 ( Water) has 34098 elements
Group 6 ( SOL) has 34098 elements
Group 7 ( non-Water) has 1096 elements
Group 8 ( Other) has 4 elements
Group 9 ( MG) has 4 elements
Group 10 ( CL) has 29 elements
Group 11 ( K) has 51 elements
Group 12 ( Ion) has 80 elements
Group 13 ( MG) has 4 elements
Group 14 ( CL) has 29 elements
Group 15 ( K) has 51 elements
Group 16 ( Water_and_ions) has 34178 elements
*Select a group: 1*
Selected 1: 'DNA'
Select group for output
Group 0 ( System) has 35194 elements
Group 1 ( DNA) has 1012 elements
Group 2 ( MG) has 4 elements
Group 3 ( CL) has 29 elements
Group 4 ( K) has 51 elements
Group 5 ( Water) has 34098 elements
Group 6 ( SOL) has 34098 elements
Group 7 ( non-Water) has 1096 elements
Group 8 ( Other) has 4 elements
Group 9 ( MG) has 4 elements
Group 10 ( CL) has 29 elements
Group 11 ( K) has 51 elements
Group 12 ( Ion) has 80 elements
Group 13 ( MG) has 4 elements
Group 14 ( CL) has 29 elements
Group 15 ( K) has 51 elements
Group 16 ( Water_and_ions) has 34178 elements
* Select a group: 1*
Selected 1: 'DNA'
Reading frame 0 time 55026.000
Precision of wi_md6.xtc is 0.001 (nm)
On Sun, Jan 20, 2013 at 7:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/20/13 7:34 AM, Mehdi Bagherpour wrote:
>
>> I use bellow commands but still in some of snapshot trajectories, two
>> strand of DNA separated from each other in VMD.
>>
>>
>> trjconv -s md.tpr -f md.xtc -o md.pdb -center
>>
>> trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -ur compact
>>
>> trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center -ur compact
>>
>> trjconv -s md.tpr -f md.xtc -o md.pdb -center -ur compact
>>
>>
> None of these involve an index group. As I said, you may have to choose
> some custom subset of atoms to serve as a centering group. The -center
> option places the geometric center of the chosen group at the center of the
> box; if there are two molecules, then the center of this group can still
> coincide with the center of the unit cell if both molecules are at opposite
> sides of the box.
>
> -Justin
>
>
>> On Sun, Jan 20, 2013 at 3:38 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 1/19/13 5:21 PM, Mehdi Bagherpour wrote:
>>>
>>> hello everybody
>>>>
>>>> I have simulated DNA using CHARMM force field for 50 ns with 2 ps
>>>> snapshots
>>>> for each step.
>>>> when I wanted to convert .xtc trajectory files to .pdb using trjconv,
>>>> some
>>>> of the snapshots were collaborated.
>>>> I have used periodic boundary conditions in this simulations.
>>>> To convert, I used bellow command:
>>>>
>>>> trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center
>>>>
>>>> In collaborated .pdb files two strands of DNA separated from each other.
>>>> when I used bellow command instead of above command, this collaborated
>>>> .pdb
>>>> file will be corrected,
>>>> but some of the other .pdb files will be ruined as same as
>>>>
>>>> trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol
>>>>
>>>> would you please help me to solve this technical problem?
>>>>
>>>>
>>>> Use -center, perhaps in conjunction with some custom index group that
>>> will
>>> serve as an adequate central group for processing.
>>>
>>> -Justin
>>>
>>> --
>>> ==============================****==========
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ==============================****==========
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> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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