[gmx-users] bilayer thickness 100ns membrane protein

[Stephani Macalino]

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?
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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>