[gmx-users] High rmsf value

[Justin Lemkul]

On 4/21/18 1:13 PM, SAYAN BHATTACHARJEE wrote:
> Dear Lemkul,
>
> My complex have two protein( Chain A & B) as dimer bound to DNA. So, I have
> to make index consisting only chain A or B, excluding DNA, then center and
> output options will both be chain A or B in  trjconv command?
> Is it possible to select both chains A & B?

The selections for centering and output are entirely separate. Center on 
chain, output whatever makes sense for your needs.

-Justin

> On Sat, 21 Apr 2018, 22:00 Justin Lemkul, <jalemkul at vt.edu> wrote:
>
>>
>> On 4/21/18 12:24 PM, SAYAN BHATTACHARJEE wrote:
>>> I bave simulated protein_dna complex for 500ns following gromacs manuals,
>>> during visualisation in vmd its doesn't maintain pbc, moves out from
>> box. I
>>> have tried those following commands, but failed to make my complex within
>>> box throughout trajectory marging protein and dna only in index.
>>>
>>> I have tried,
>>>
>>> 1. Trjconv -f 500ns.xtc -s md_0_1.tpr -pbc cluster -n protein_dna.ndx -o
>>> center.xtc -ur compact  -center
>>>
>>> Auto select protein_dna from input index for both centering and output.
>>>
>>> I have tried -pbc mol option too but it didn't work here.
>>> Visualisation in vmd is now fine(using cluster option and loading
>>> center.xtc trajectory), complex is now within box, but, in the next step
>>> when I tried nojump option and fit with reference initial structure by
>>> uising the following commands, pbc condition didn't maintain and protein
>>> motion was horrible and the rmsf shows very high value(using  fit.xtc/
>>> nojump.xtc/ centre.xtc for rmsf calculation).
>>>
>>> 2.Trjconv -f center.xtc -s md_0_1.tpr -pbc nojump -n protein_dna.ndx -o
>>> nojump.xtc
>>>
>>> 3.Trjconv -f  nojump.xtc -s md_0_1.tpr -fit rot+trans -n protein_dna.ndx
>> -o
>>> fit.xtc
>>>
>>> Please give suggestions in this regard.
>>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
>>
>> If you have a complex, don't try to center on the entire thing. Choose
>> one chain of the complex and center on that. If elements of the complex
>> are split on opposing "faces" of the box, their center is still
>> (geometrically speaking) coincident with the actual center of the box,
>> so trjconv works properly but it's not what you want.
>>
>> -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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-- 
==================================================

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

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