[gmx-users] reference structure of g_rms

[Hsin-Lin Chiang]

Hi Tsjerk,

It's very helpful information.
Thank you very much

Sincerely yours,
Hsin-Lin
Hi 
Hsin-Lin,

If you use a .tpr file, you perform a mass-weighted fit and 
analysis.
A .gro file has no masses and thus the fit and analysis are 
performed
non-mass weighted, which will give differences, depending on 
the
selection for the 
analysis.

Hope it 
helps,

Tsjerk

2011/8/17 Hsin-Lin Chiang <jiangsl at 
phys.sinica.edu.tw>:
>> > 
Hi,
>> 
>
>> > I got confused about the choice of reference structure of 
g_rms. 
(g_rms
>> > 
-s)
>> > For 
example,
>> > I run MD after 
PR.
>> > That's means md.tpr was generated from 
pr.gro
>> > I tried to use pr.gro and md.tpr to be the reference 
structure but 
get
>> > different 
result.
>> > I think these two should cause the same 
result.
>>
>> I think they should give the same result. If not, then the 
mostly 
likely
>> explanation is that you've not used the files the way you think 
you 
have.
>> You need to be able to 
issue
>>
>> grompp -f md -c pr -o 
md
>> g_rms -s md.tpr -f 
whatever
>> g_rms -s pr.gro -f 
whatever
>>
>> and get different results for there to be some kind of problem. 
In 
any
>> case, you need to provide copies of your command lines and the 
different
>> result in order for us to see whether you or GROMACS has done 
something
>> wrong/unexpected/whatever. Otherwise it's hearsay and we'll 
shrug and 
do
>> something else with our time 
:-)
>>
>> 
Mark
> 
Hi,
>
> I checked the result 
again
> The order of the different is less than 0.1 
nm.
> So that means this different is caused by 
precision?
>
> Sincerely 
yours,
> 
Hsin-Lin
>

 
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