[gmx-users] reference structure of g_rms

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Aug 17 18:24:55 CEST 2011

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,


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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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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