Re: [plumed-users] Differences in ALPHARMSD values using MetaD and RESTRAINTS

[Giovanni Bussi]

Hello,

Not sure I understand the question.

You are talking about two different simulations, so results can indeed differ. They use the same CV, but in one case you apply metadynamics on it, in the other case you apply a restraint.

Can you check the trajectory of both simulations visually to see if an alpha helix is present also in the second simulation?

Giovanni

On 3 Feb 2026, at 16:02, Carlos Henrique <carlos.qu...@gmail.com> wrote:

Dear Colleges, 

I have combined METAD and US in my simulations. However, anomalies have come out. Recently, I noticed significative differences in ALPHARMSD values from METAD and RESTRAINT, using the same system and plumed setup in both cases, via GROMACS. For instance, while METAD delivers values around 15.2, RESTRAINTS displays values around 1.5, which is not coherent with the system. I have looked for additional information in order to sort it out, but I have not found any valuable advice.

Below, part of the METAD and RESTRAINT plumed files.

WHOLEMOLECULES ENTITY0=1-421
MOLINFO MOLTYPE=protein STRUCTURE=reference.pdb
helix: ALPHARMSD RESIDUES=25-39,4-16 TYPE=OPTIMAL R_0=0.1 NOPBC 

METAD ...
ARG=helix
PACE=1000  
HEIGHT=1.2 
SIGMA=0.10
BIASFACTOR=10
FILE=HILLS
GRID_MIN=5
GRID_MAX=18
... METAD

WHOLEMOLECULES ENTITY0=1-421 
MOLINFO MOLTYPE=protein STRUCTURE=reference.pdb
helix: ALPHARMSD RESIDUES=25-39,4-16 TYPE=OPTIMAL R_0=0.1 NOPBC
cst: RESTRAINT ARG=helix AT=15.251875 KAPPA=200.0,200.0

Any suggestion is welcome!

All the best,

Cruz

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[Carlos Henrique]

Hi Giovanni,

Thank you for your reply.

Yes, METAD and RESTRAINT simulations of the same system using the same CV, but delivering large differences in CV values. At that time, I worried if it could be an internal issue, but actually I have given different reference structures, justifying such incoherent results. Now, it's working properly. 

Sorry for spending your valuable time on this, and I really appreciate your help.

Have a lovely day.

Best regards,

Cruz

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