[gmx-users] peptide ligand

[Justin Lemkul]

On 11/10/17 11:22 AM, farial tavakoli wrote:
>   blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Then I ignore that  i cant visualize the protein motion in vmd and go on the left steps of the results quality assuranc?

Watching the trajectory is the most important part of the simulation. 
You need to have matching coordinate and trajectory files.

-Justin

>
> Sent from Yahoo Mail for iPhone
>
>
> On Friday, November 10, 2017, 7:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 11/10/17 11:02 AM, farial tavakoli wrote:
>>    blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  so how come i bring the .gro and newtrj.xtc files in the vmd , my protein doesnt move at all? I think , it is because of the .gro file has protein, ligand and sol cordinates , but the newtrj.xtc has just my protein and ligand. Am i right?
>>    
> Your trajectory and coordinates have to match if you want to visualize.
> If there's a mismatch, VMD prints a clear error that should tell you of
> that fact.
>
> -Justin
>
>>        On Friday, November 10, 2017, 7:20:48 PM GMT+3:30, Justin Lemkul <jalemkul at vt.edu> wrote:
>>    
>>    
>>
>> On 11/10/17 10:35 AM, farial tavakoli wrote:
>>> Dear Justin
>>>
>>> Thank you for replying
>>>
>>> This is my input xtc file :
>>>
>>> gmx check -f md_0_1.xtc
>>>
>>> Checking file md_0_1.xtc
>>> Reading frame       0 time    0.000
>>> # Atoms  49582
>>> Precision 0.001 (nm)
>>> Last frame       1000 time 10000.000
>>>
>>>
>>> Item        #frames Timestep (ps)
>>> Step          1001    10
>>> Time          1001    10
>>> Lambda           0
>>> Coords        1001    10
>>> Velocities       0
>>> Forces           0
>>> Box           1001    10
>>>
>>> and this is my output xtc file:
>>>
>>> gmx check -f newtrj.xtc
>>>
>>> Checking file newtrj.xtc
>>> Reading frame       0 time    0.000
>>> # Atoms  3378
>>> Precision 0.001 (nm)
>>> Last frame       1000 time 10000.000
>>>
>>>
>>> Item        #frames Timestep (ps)
>>> Step          1001    10
>>> Time          1001    10
>>> Lambda           0
>>> Coords        1001    10
>>> Velocities       0
>>> Forces           0
>>> Box           1001    10
>>>
>> These outputs do not support your assertion that newtrj.xtc only
>> contains one frame. Clearly both the old and new trajectories have the
>> full 1001 frames.
>>
>> -Justin
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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