A problem about setting the parameter HEIGHT of the well-tempered MetaD Bias

[Hang LYU]

Dear all,

     I am trying to repeat a well-tempered MetaD simulation reported in a paper(Chem. Mater. 2020, 32, 529−536). The part in the paper describing the parameters of the well-tempered MetaD is shown in the following picture. It is said in the paper that the height of the bias is set to ~2kb·T. I checked the manual of plumed-2.7 and found the key word HEIGHT. However, I am still not very clear about the unit of the key word. Does HEIGHT=2 refer to that the height of the Gaussian bias potentials is set to ~2 kb·T?

Best wishes,

Hang LYU

PS:

The command I used to specify the parameters.

METAD ARG=CV1,CV2 SIGMA=0.5,1.0 HEIGHT=2 PACE=500 BIASFACTOR=300 TEMP=400.0 LABEL=wtmetaD RESTART=AUTO

[Carlo Camilloni]

Plumed units are kJ/mol, nm, ps unless specified by using the UNITS keyword, so HEIGHT=2 is 2 kJ/mol

https://www.plumed.org/doc-master/user-doc/html/_syntax.html

On 22 Feb 2021, at 16:06, Hang LYU <terryh...@gmail.com> wrote:

Dear all,

     I am trying to repeat a well-tempered MetaD simulation reported in a paper(Chem. Mater. 2020, 32, 529−536). The part in the paper describing the parameters of the well-tempered MetaD is shown in the following picture. It is said in the paper that the height of the bias is set to ~2kb·T. I checked the manual of plumed-2.7 and found the key word HEIGHT. However, I am still not very clear about the unit of the key word. Does HEIGHT=2 refer to that the height of the Gaussian bias potentials is set to ~2 kb·T?

<WeChat Screenshot_20210222204559.png>

Best wishes,

Hang LYU

PS:

The command I used to specify the parameters.

METAD ARG=CV1,CV2 SIGMA=0.5,1.0 HEIGHT=2 PACE=500 BIASFACTOR=300 TEMP=400.0 LABEL=wtmetaD RESTART=AUTO

--
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 view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/826bcb3a-f85f-4e3e-98a1-a121d8c0aff6n%40googlegroups.com.
<WeChat Screenshot_20210222204559.png>

[Hang LYU]

Dear Carlo,

   Thanks for your answer. But I am still not clear about how to set the height of Gaussian bias potential to 2kB·T, because the unit of 2kb·T is kJ (or eV) which cannot be transform into kJ/mol. I also notice another keyword TAU in the manual of plumed-2.7. I am wondering whether I can set the height of Gaussian bias potential to 2kb·T by specifying PACE=500, TAU=500 in plumed in put file, and set timestep to 2 fs in LAMMPS. But it seems like that it is kB·ΔT not kB·T.

Best wishes,

Hang LYU

[Omar Valsson]

Hello Hang, 

For example, 300 K is roughly 2.5 kJ/mol (e.g., see Table 1 here https://cccbdb.nist.gov/thermo.asp)

You can also use the kt command line tool (https://www.plumed.org/doc-master/user-doc/html/kt.html):

plumed kt --temp 300.00 -> "When the temperature is 300.000000 kelvin kT is equal to 2.494339 kj/mol”

Regards,

Omar

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/1c344062-9559-4b55-a018-f7cb2dada874n%40googlegroups.com.

[Hang LYU]

Dear Omar,

     Thanks very much for your answer.

Best wishes,

Hang LYU