[gmx-users] Same values are showing when tried to plot rmsd

[Erik Marklund]

Justin A. Lemkul skrev:
> Quoting minnale <minnale_gnos at rediffmail.com>:
>
>   
>> Thanks for your prompt reply to Erik and Florian
>> i have done according to Erik's reply but there is no change in the RMSD
>> values
>> iam mentioning what i have done
>>
>> 1.make_ndx -f protein.gro -o calpha_re20_90.ndx
>>  selected 3 & r 20-90 ( 3 = calpha)
>>
>> this ndx gave input for g_rms
>> g_rms -f 7nsprot.xtc -n calpha_re20_90.ndx -pbc -s minwat -o rms_calpha.xvg
>>   selected calpha_res20-90 for least square fit
>>   selected calpha for RMSD
>> but there is no difference in RMSD values of protein, selected
>> protein&res20-90(index for segment) and calpha&res20-90(suggested one)
>>
>> have i made any mistake in mentioning options in commands
>>     
>
> Yes, as Erik already mentioned, you must use the calpha_res20-90 group for both
> the fitting and the calculation.  What you're showing is essentially the same
> thing you already showed in your previous message - you are calculating the
> RMSD of the entire 'calpha' group for the protein.
>
> -Justin
>
>   
Hi,

And I shold point out that, depending on what exactly you are 
investigating, the group used for the lsq fit can be either the calphas 
from your subset of residues or all of the calphas. The two alternatives 
will tell you different things.

/Erik
>> Thanks in advance.
>>
>> On Mon, 02 Jun 2008 Erik Marklund wrote :
>>     
>>> minnale skrev:
>>>       
>>>>  Hi all,
>>>> I have run the protein in water for 7ns and plotted RMSD for whole protein
>>>>         
>> with 250 residues and segmented 70 residues out of 250 residues by using
>> index file, result in two cases values are nearly same and showing almost
>> same graph. I think it should be different in two cases.
>>     
>>>> the commands I have given for whole protein and segmented protein are
>>>>
>>>> g_rms -f 7ns_pro.xtc -pbc -s min_pro.tpr -o rms_whol7nsprot
>>>>   selected c-alpha for least square fit
>>>>   selceted c-alpha for RMSD calculation
>>>>
>>>> g_rms -f 7ns_pro.xtc -pbc -s min_pro.tpr -n 20_90res.ndx -o rms_segm7nsprot
>>>>   selected 20_90res for least square fit
>>>>   selected c-alpha for RMSD calculation
>>>>
>>>> Any suggestions are appreciated
>>>> Thanks in advance
>>>>
>>>>
>>>>
>>>> Swiss
>>>>         
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>>>>         
>>> Hi,
>>>
>>> You have in fact calculated RMSD for all calphas in both cases, but only
>>>       
>> used a subset of them for fitting in the second case. You need to create an
>> index group for the calphas in your segment and use that for your calculation
>> (and fitting).
>>     
>>> -- -----------------------------------------------
>>> Erik Marklund, PhD student
>>> Laboratory of Molecular Biophysics,
>>> 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://xray.bmc.uu.se/molbiophys
>>>
>>>       
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
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://xray.bmc.uu.se/molbiophys