[gmx-users] shift in trajectory

[Justin Lemkul]

On 10/18/19 4:23 AM, Amin Rouy wrote:
> Dear Justin,
>
> Yes, they form a clear phase separation.
> Well, I did not clearly understand your last suggestion. I do not need to
> have their COM coordinate, I need COM of 'A' stays in the middle of the
> box.

I suggested looking at the COM coordinates as a means of checking your 
assumptions about where the species are in the box. That way you can 
better understand whether or not you're getting the behavior you expect. 
I understand exactly what you're after and it should be straightforward 
to do.

-Justin

> On Thu, Oct 17, 2019 at 5:17 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 10/17/19 8:04 AM, Amin Rouy wrote:
>>> Dear Justin,
>>>
>>> I have a two-component system (they demix), which are grouped as  'A' and
>>> 'B' from beginning of the simulation. Now my trajectory is asymmetric
>> with
>>> respect to the center. I can make it symmetric with gmx trjconv flag
>> -shift
>>> manually, but I need to apply the flag -center to get the 'A' component
>>> sitting exactly at the center of the box.
>>>
>>> So having my index file, what I do is:
>>>
>>> 1- *gmx trjconv -f NPT.xtc -o NPT-centered.xtc -pbc none -n index.ndx*
>>>
>>> and I select whole system.
>> Making molecules whole should always be the first step. I disagree with
>> the previous advice you were given to use this PBC option first.
>>
>>> 2- *gmx trjconv -f NPT-centered.xtc -o NPT-centered2.xtc -n index.ndx
>>> -center*
>>>
>>> and I select group 'A' for Select group for centering, and whole system
>> for
>>> Select group for output.
>>>
>>> 3- *gmx trjconv -f NPT-centered2.xtc -o NPT-centered3.xtc -n index.ndx
>> -pbc
>>> mol -s NPT.tpr *
>>>
>>> and here I select whole system.
>>>
>>>
>>> What I get is the same trajectory as I had in the beginning, no change at
>>> all. I can see it with vitalizing and moreover from gmx density outcome.
>> Do you get a clear phase separation with a layer of A and a layer of B
>> in the simulation? In steps prior to separation, it will not be apparent
>> that the molecules are actually centered, but you can obtain their COM
>> coordinates with gmx traj -ox -com and confirm that they correspond to
>> the box center.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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