[gmx-users] bilayer thickness 100ns membrane protein

[Justin Lemkul]

On 9/17/18 9:57 PM, Stephani Macalino wrote:
> Hello again,
> I have pinpointed the problem I have.
> I tried to follow
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
> .
> But I only used pbc whole, nojump and mol center.
> After I used nojump, the thickness values of my trajectory is stable at
> around 40. After I use -pbc mol - center, the strange value jumps are
> observed.
> I want to know if it is okay to just leave off the mol center?

There is no one-size-fits-all or "required" set of trjconv commands. 
Visualize the output. If the molecules are properly re-imaged, you don't 
need to do anything else.

-Justin

> Hope you can help. Thank you!
> Regards,
> Stephani
>
> On Mon, 17 Sep 2018 at 06:47, Stephani Macalino <stephanimacalino at gmail.com>
> wrote:
>
>> Hello,
>> Thanks for the response. But I have already done the trjconv pbc whole,
>> nojump and center for my system to possibly fix this. Lemme try to check
>> again from my orig trajectory file.
>> Then I will get back to you.
>> Thank you!
>>
>> On Mon, Sep 17, 2018, 01:27 Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>> On 9/16/18 12:16 PM, Stephani Macalino wrote:
>>>> Hello,
>>>> I ran a 100ns MD or a membrane protein and am now analyzing the APL and
>>>> bilayer thickness from the trajectory file of 50,000 frames.
>>>> When I graphed the values, around 20 to 30k frames in (and some frames
>>>> along 40k) the value jumps from 40 to 70. The rest of the frames have
>>>> pretty similar value at 40.
>>>> Can you provide any idea why this happens?
>>>> I already used trjconv in for my system before doing this.
>>> Have you visualized the trajectory to make sure all molecules were
>>> imaged appropriately? It sounds to me like your lipids are simply
>>> jumping across PBC. Sudden jumps or discontinuities in time series are
>>> almost always due to PBC effects.
>>>
>>> -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.thelemkullab.com
>>>
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>>>
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-- 
==================================================

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.thelemkullab.com

==================================================