[gmx-users] regarding rmsd calculaton

[Justin Lemkul]

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
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Virginia Tech Department of Biochemistry
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