[gmx-users] Dimer g_rms

[Erik Marklund]

XAvier Periole skrev:
>
> On Jun 30, 2010, at 10:34 AM, Carla Jamous wrote:
>
>> Dear all,
>>
>> I'm running my first simulation of a dimer.
>> When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha) 
>> to get the RMSD of the whole dimer, the graph is ascending, till 
>> reaching a value of 8 A.
>> in this case, I take a .tpr file, a .xtc file and a .ndx file of the 
>> whole dimer.
>>
>> However, when I run g_rmsd on Calpha, but this time, to get the RMSD 
>> of one chain (one monomer), the graph is constant with value around 1 
>> A. and this for both chains, when taken alone.
>> In this case, I take a .tpr file, a .xtc file and a .ndx file of the 
>> monomer.
>>
>> So is this an error of using g_rms?
> Well this is not an error. Evidently your monomers are stable 
> (rmsd~0.1nm)
> and you dimer is not.
> This might be result of either an actual deformation of the dimer or
> one of your monomer is crossing the periodic boundaries and thereby
> the rmsd is not representative.
> try to trjconv your trajectory using the -pbc nojump and run g_rms again.
I suspect the former. If pbc crossing is the explanation, then it would 
show up in the analysis of one of the monomers.

Erik
>>
>> Thank you.
>>
>> Carla
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-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/