[gmx-users] Dimer g_rms

[XAvier Periole]

On Jun 30, 2010, at 12:47 PM, Erik Marklund wrote:

> 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.
Not necessary!
If the dimer separates across the boundaries you have
a problem of fitting the two together while they are separated.
This is only if you use the dimer. The monomers would be fine.

The indication that it is the former comes from the rmsd that
seem to increase gradually up to 0.8 nm.
>
> 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/
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