[gmx-users] Re: Regarding mean square displacement

Justin Lemkul jalemkul at vt.edu
Thu Feb 7 12:24:08 CET 2013

On 2/6/13 11:49 PM, Kavyashree M wrote:
> Dear users,
> Since I am getting the mean square displacements in terms of
> several nm^2. I doubt it is wrong. Could anyone please explain
> me the solution for this. I checked the structure it is not denatured,
> In addition I used -rmcomm in order to remove the COM movements.

Sounds like a PBC issue.  Does your dimer split across periodic boundaries?  If 
it does, then your MSD is going to go through the roof because it's measuring 
the MSD of the whole protein.


> On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
>> Dear users,
>>   I have a very basic question in MSD calculation.
>> g_msd calculation on a protein dimer (~237 aa each)
>> trajectory gave a plot of msd, with the values ranging
>> between 1 to 14nm^2.
>> But is this a sensible MSD? As the values given in a
>> paper i was referring was in Ang^2
>> J. Chem. Theory Comput. 2012, 8, 1129-1142
>> Command that i used -
>> echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000
>> -e 50000 -rmcomm
>> Is the range of diffusion coefficient of proteins of in water l
>> in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)
>> Thank you
>> kavya


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list