[gmx-users] regarding rmsd calculaton

[shakuntala dhurua]

during rdf calculation i used flag gmx rdf -n .ndx -o .xvg -f .xtc -s .tpr
it prompt Specify a selection for option 'ref' then i had given one one
reference group 17 then it appear Selection '17' parsed then  any number of
selections for option 'sel' again it apper Selection '19' parsed .how can i
solve this rdf calculation please suggest me.


On Fri, Nov 1, 2019 at 8:40 PM shakuntala dhurua <madhu.dhurua94 at gmail.com>
wrote:

> thank you sir
>
> On Thu, Oct 31, 2019 at 3:37 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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.
>> >>>>> --
>> >>>>> Gromacs Users mailing list
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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
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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>