[gmx-users] regarding rmsd calculaton

[Justin Lemkul]

On 10/31/19 6:02 AM, shakuntala dhurua wrote:
> thank you sir, by this gmx trjconv -center -pbc mol the two chains are
> coming closer but still rmsd result is high and fluctuating highly while
> taking two chain at a time. please suggest me to calculate resonable rmsd
> value for full protein

If you have very flexible regions, the RMSD value will be high. That's 
not necessarily wrong. If you've corrected the imaging issue that led to 
spurious increases in RMSD, this is the actual value. Whether or not it 
makes sense to consider the dimer as a whole in RMSD is another issue, 
but it depends on what you want to calculate and you need to be 
judicious in your selections for fitting and calculation groups, 
especially in the case of flexible termini or disordered regions.

-Justin

> On Wed, Oct 30, 2019 at 7:52 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 10/30/19 9:39 AM, shakuntala dhurua wrote:
>>> i have generated trr file for a protein containing two chains .during the
>>> simulation two chains are going at two different sides of the box. so the
>>> RMSD results are abruptly high (near 35-40 angstrom). To create a image
>> of
>>> one chain at the same side of other chain,i used the following command by
>>> removing pbc
>>> ==============
>>> try1. trjconv -s .tpr -f .trr -o .xtc -pbc mol -ur compact
>>> try2.trjconv -s tpr -f .trr -o .xtc -pbc nojump
>>> try3. -f a.mdp -c a_cluster.gro -o a_cluster.tpr
>>> try4  trjconv -s a.tpr -f .trr -o xtc -fit rot+trans
>>> ==============================
>>> still similar results are coming. but for each chain,RMSD value is
>>> reasonable.
>>> kindly suggest some way to calculate RMSD value for full protein
>> Create an index group for one protein and use it to center the
>> coordinates. This will re-wrap the whole complex into the central image.
>> gmx trjconv -center -pbc mol
>>
>> -Justin
>>
>>> On Wed, Oct 30, 2019 at 4:59 PM rajat punia <rjtpunia at gmail.com> wrote:
>>>
>>>> make sure you superimpose the structures using -fit flag.
>>>>
>>>>
>>>> On Wed, 30 Oct 2019 at 16:39, shakuntala dhurua <
>> madhu.dhurua94 at gmail.com>
>>>> wrote:
>>>>
>>>>> actually I am using insulin protein system, i have calculated rmsd but
>>>> that
>>>>> is too high which is approx 40 amstrong which is not supposed to be ,
>> and
>>>>> initially during energy minimization two chain go far away from each
>>>> other.
>>>>> I have used flag like trjconv -s .tpr -f .trr -o .xtc -pbc mol -ur
>>>> compact
>>>>> trjconv -s .tpr -f .trr -o .xtc -pbc nojump etc but still result is
>> same
>>>> .
>>>>> so please suggest me to solve this problem.
>>>>> --
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>>>> --
>>>> *Regards,*
>>>> *Rajat Punia*
>>>> *PhD Chemical Engineering*
>>>> *IIT Delhi*
>>>> *+91-9821210386*
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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
>>
>> ==================================================
>>
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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

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