[gmx-users] regarding rmsd calculaton

[shakuntala dhurua]

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


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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