Coordination no. as CV in metadynamics

[Sukriti Gupta]

Hi,

I was trying to run a simulation with one metal ion and one sulphate in water. I wanted to see the free energy for sulphate ions to reach first solvation shell of metal ions by replacing one water molecule present in 1st solvation shell of metal ion. So I took metal ion - water coordination no. as one CV and sulphate - metal ion distance as another CV. Here coordination no. should change only one or two units in the simulation, when sulphate ion comes closer to metal ion. But in this simulation, I find coordination no. to reduce a lot (becomes 2,1 or even 0.6 etc.) and trajectory shows water molecules getting removed from 1st solvation shell of metal ion. Does anyone have any idea as to what can be the problem. Isn't metadynamics only supposed to show the steps which are physically possible. My plumed.dat file is as follows:
 
dist: DISTANCE ATOMS=1,2
coor: COORDINATION GROUPA=1 GROUPB=7-1527 SWITCH={EXP R_0=0.5 D_0=0.217 D_MAX=0.3 STRETCH}
METAD ...
LABEL=metad
ARG=dist,coor
PACE=1000
HEIGHT=3
SIGMA=0.03,0.3
FILE=HILLS
... METAD
PRINT STRIDE=500 ARG=dist,coor,metad.bias FILE=COLVAR

Thanks and Regards
Sukriti

[Sukriti Gupta]

Can anyone please help...

[Pablo Piaggi]

Dear Sukriti,

Your choice of collective variables seems reasonable to me. Nevertheless there is no way to know a priori if they will work.

You say that the coordination number reduces a lot during the simulation and that you weren't expecting this behavior. You should check if you have defined the CV's properly before running biased simulations, otherwise they will be meaningless. A quick way to check them is having an initial and a final configuration and calculating the value of the CV's for them. Afterwards perhaps it is a good idea to do an unbiased simulation.

Moreover, I see something strange in your plumed.dat file. The D_MAX keyword represents a distance beyond which the switching function (in your case EXP) is negligible. You have chosen a value of 0.3 for this parameter but the switching function is still very large at this point. You should plot it and see for yourself. I would employ a value of around 3.0 for your choice of R_0 and D_0 (without knowledge of the system I assume they are properly chosen).

Regarding your last question "Isn't metadynamics only supposed to show the steps which are physically possible?". Yes, metadynamics will represent "physically possible" paths provided that you choose the right collective variables and the appropriate parameters.

Regards,

Pablo

--
You received this message because you are subscribed to the Google Groups "PLUMED users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users...@googlegroups.com.
To post to this group, send email to plumed...@googlegroups.com.
Visit this group at http://groups.google.com/group/plumed-users.
To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/112372c9-2943-45da-acd8-6ec62b1ec643%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Sukriti Gupta]

Dear Pablo,

Thanks for the reply. I kept the metal atom frozen and changed the definition on coordination no. as following:

coor: COORDINATION GROUPA=1 GROUPB=7-1527:3 SWITCH={RATIONAL R_0=0.05 D_0=0.23 NN=6 MM=12 D_MAX=0.35 STRETCH} NLIST NL_CUTOFF=4 NL_STRIDE=100

The final fes.dat which I get is fine and I am able to get the desired result.

On the other hand when I change the metal ion, I find that if I bias only distance and not coordination no., I get the desired result i.e. coordination between water molecules and metal in the simulation change only by 1 or 2 units when sulphate comes closer to vanadium. But when I bias coordination nos. also, my coordination nos. changes a lot. Also in the trajectory as well I see same changes in the coordination no. as shown in the COLVAR file at a particular step. Does that mean that the strength of coordination between water and this metal is very less and it can be easily removed by adding small amount of energy to the system. Also I tried to reduce the HILLS value for coordination no. to as low as 0.005, but still I faced the same problem. Can anyone please help me with this.

Regards
Sukriti

[Pablo Piaggi]

Dear Sukriti,

I believe your question was already answered by Gareth Tribello as a reply to the topic "Adding small energies to collective variable coordination no. in MetaD".

Regards,

Pablo