[gmx-users] Regarding RMSD analysis result

naga sundar naga25sundar at gmail.com
Tue Sep 25 10:08:31 CEST 2012

Dear Felipe

                Thanks for ur reply.

         The system is a protein-protein complex. Like u r saying its due
to pbc problem then why any abnormality  doesn't happened to the native
complex (Black line)?.  As already suggest by justin i checked  the pbc
conditions upto my knowledge everything is fine. of-course this is not the
first MD run for these native and mutant complexes. I run twice and got the
same results.

        I want know this kind of RMSD is rite r wrong?..

On Tue, Sep 25, 2012 at 12:45 AM, Felipe Pineda, PhD <
luis.pinedadecastro at lnu.se> wrote:

> It looks for me like the known pbc effect others already pointed to. If
> you have just a protein-ligand complex (+ water and counterions of course)
> it's relatively easy to manually (a piece of code would do it) bring the
> ligand to the correct position in the frames showing an abnormally high
> value by subtracting half the x/y dimension of the box from its coordinates
> and re-calculate the rmsd , but I think trjconv would do it as well.
> Felipe
> On 09/25/2012 09:22 AM, naga sundar wrote:
>> Dear justin
>>                  http://rmsdnagasundaram.**blogspot.in/<http://rmsdnagasundaram.blogspot.in/>.
>> This is the link to
>> my rmsd graph. Plz check it once and suggest me.
>> Thanks
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