13 Replies to “CL&P Force Field for Ionic Liquids”
First of all, I would like to say that this is a great work being accomplished by this group.
Secondly, I have a doubt about the parametrization of the PF6- anion, I know that the .ff files have the citations of the articles from which the bonds and angles parameters are taken, however I noticed that in the AMBER parametrization of this anion it is usual to consider two terms in the angles harmonic potentials, both with the same force constants but with different equilibrium angles: 90 and 180 degrees.
The force field provided in the files has just one term with the equilibrium angle of 90 degrees. I would like to know if just this single term in the angles part of the potential exists or if it is necessary to add the other term with the other equilibrium angle. In fact, I’m doing some molecular dynamics in LAMMPS and the potential energy is indeed to high with the angles potential contributing with most of it.
Hello,
In PF6- there is ambiguity because F-P-F angles can have two values: 90 and 180. Thus there are three 180 degree angles that should not be included. Recent versions of the force field tool (https://github.com/agiliopadua/fftool) will not include the 180 angles automatically when generating input files for MD simulations.
Agilio
Dear prof. Padua, first of all I want to congrat for this work, which has been very helpful for me.
Secondly, I have a question about some parameters of the force field. Basically, I can’t find a corrispondence between some parameters as they are published in J. Phys. Chem. B 2004, 108, 2038-2047 (plus. supp. info) and those ones I’ve found in github.com. For example, in github I find:
[bonds]
Cr-Na 1.315 3992
but in the article the value of the constant for this bond is 1996 KJ/(mol A^2). This happens for various bonds and angles constants. Plus, some authors that have done force fields based on yours report the github values in their articles (es. Zhao 2007), but others use the article ones (es. Kodderman 2007). Is there something I’m missing?
Thank you for your answer, this would really help me.
Unfortunately some mistakes crept into the papers. Sorry for that.
One common is dividing harmonic force constants by 2 (some codes and force fields to it like that).
Normally the values in the files on GitHub are the good ones.
Don’t hesitate to ask in case of doubt.
Dear prof. Padua, firstly I want to congratulate for this excellent contribution,great work was done by this group ,it helped me a. lot in my research.
I Wanted to ask that is there any tool and force field available to simulate nanoparticles?just like your othrs tool like fftool,Force field for ionic liquids.??
Thanks. Maybe you will have to write a small script to place the atoms in the right positions to create a NP, or look for a tool that can do that. fftool could do it if supplied with a xyz file and a force field file with the right parameters. Avogadro or VESTA can maybe help to create the nanoparticle.
Thanks sir for your suggestion,actually I have nanoparticle in xyz format but i need the forcefield,actually i want to add nanoparticle in the ionic liquid. For simulating ionic liquid individually i used the fftool and il.ff ,so in order to add some some nanopartcles i need the forcefield…parameters which are absent in oplsaa.fa .(error: force field file 150.00000000 not found)
will it be possible If i can add lj parameters in the oplsaa.ff file??
You are not asking the right question. What kind of nanoparticle? What element(s)? What structure, size, etc.
Then you have to research the literature for the atomistic parameters. There are many possible interatomic potentials for metals, etc. A simple tool to build simulation boxes will not solve your problem.
Dear Prof. Padua, firstly i want to congratulate for this excellent work, which has been very helpful for me in my research.
Secondly, i have some questions about MD of ILs. I am simulating the ILs system ([Mmim][NTf2]) using your developed force field in DL_POLY software， the error (r14>rcut) occur and the simulation is stop, could you help me?
Thank you for your answer, it would really help me.
Kind regards
Yongji Guan
Dear Prof. Padua, first of all, congratulations for your work. I’m a new student of theoretical chemistry and i will work with molecular dynamics, specifically with solvatation of proteins by ionic liquids. Your work will be very usefull for me, but i have a problem. I need use NAMD to perform my simulations, because i will study the solvation using minimum-distance distribution functions and to do this i will use a software (that was develop by our reasearch group) that read the archives in a format for NAMD ( that is why i need use namd) . I saw that the topology and the parameters are in the format fo GROMACS. Is there a way to,based on theses files, rewrite them for NAMD ?
Kind Regards
Vinicius Piccoli
I don’t use NAMD so I don’t know the details of the file formats. I would find strange that a utility is not available to convert between Gromacs and NAMD-Charmm formats.
First of all, I would like to say that this is a great work being accomplished by this group.
Secondly, I have a doubt about the parametrization of the PF6- anion, I know that the .ff files have the citations of the articles from which the bonds and angles parameters are taken, however I noticed that in the AMBER parametrization of this anion it is usual to consider two terms in the angles harmonic potentials, both with the same force constants but with different equilibrium angles: 90 and 180 degrees.
The force field provided in the files has just one term with the equilibrium angle of 90 degrees. I would like to know if just this single term in the angles part of the potential exists or if it is necessary to add the other term with the other equilibrium angle. In fact, I’m doing some molecular dynamics in LAMMPS and the potential energy is indeed to high with the angles potential contributing with most of it.
Hello,
In PF6- there is ambiguity because F-P-F angles can have two values: 90 and 180. Thus there are three 180 degree angles that should not be included. Recent versions of the force field tool (https://github.com/agiliopadua/fftool) will not include the 180 angles automatically when generating input files for MD simulations.
Agilio
Dear prof. Padua, first of all I want to congrat for this work, which has been very helpful for me.
Secondly, I have a question about some parameters of the force field. Basically, I can’t find a corrispondence between some parameters as they are published in J. Phys. Chem. B 2004, 108, 2038-2047 (plus. supp. info) and those ones I’ve found in github.com. For example, in github I find:
[bonds]
Cr-Na 1.315 3992
but in the article the value of the constant for this bond is 1996 KJ/(mol A^2). This happens for various bonds and angles constants. Plus, some authors that have done force fields based on yours report the github values in their articles (es. Zhao 2007), but others use the article ones (es. Kodderman 2007). Is there something I’m missing?
Thank you for your answer, this would really help me.
Kind regards,
Matteo Busato
Hi,
Unfortunately some mistakes crept into the papers. Sorry for that.
One common is dividing harmonic force constants by 2 (some codes and force fields to it like that).
Normally the values in the files on GitHub are the good ones.
Don’t hesitate to ask in case of doubt.
Regards,
Agilio
Dear prof. Padua, firstly I want to congratulate for this excellent contribution,great work was done by this group ,it helped me a. lot in my research.
I Wanted to ask that is there any tool and force field available to simulate nanoparticles?just like your othrs tool like fftool,Force field for ionic liquids.??
THANKS
Thanks. Maybe you will have to write a small script to place the atoms in the right positions to create a NP, or look for a tool that can do that. fftool could do it if supplied with a xyz file and a force field file with the right parameters. Avogadro or VESTA can maybe help to create the nanoparticle.
Thanks sir for your suggestion,actually I have nanoparticle in xyz format but i need the forcefield,actually i want to add nanoparticle in the ionic liquid. For simulating ionic liquid individually i used the fftool and il.ff ,so in order to add some some nanopartcles i need the forcefield…parameters which are absent in oplsaa.fa .(error: force field file 150.00000000 not found)
will it be possible If i can add lj parameters in the oplsaa.ff file??
You are not asking the right question. What kind of nanoparticle? What element(s)? What structure, size, etc.
Then you have to research the literature for the atomistic parameters. There are many possible interatomic potentials for metals, etc. A simple tool to build simulation boxes will not solve your problem.
Dear Prof. Padua, firstly i want to congratulate for this excellent work, which has been very helpful for me in my research.
Secondly, i have some questions about MD of ILs. I am simulating the ILs system ([Mmim][NTf2]) using your developed force field in DL_POLY software， the error (r14>rcut) occur and the simulation is stop, could you help me?
Thank you for your answer, it would really help me.
Kind regards
Yongji Guan
Maybe you are using a cutoff that is too small.
Dear Prof. Padua, first of all, congratulations for your work. I’m a new student of theoretical chemistry and i will work with molecular dynamics, specifically with solvatation of proteins by ionic liquids. Your work will be very usefull for me, but i have a problem. I need use NAMD to perform my simulations, because i will study the solvation using minimum-distance distribution functions and to do this i will use a software (that was develop by our reasearch group) that read the archives in a format for NAMD ( that is why i need use namd) . I saw that the topology and the parameters are in the format fo GROMACS. Is there a way to,based on theses files, rewrite them for NAMD ?
Kind Regards
Vinicius Piccoli
I don’t use NAMD so I don’t know the details of the file formats. I would find strange that a utility is not available to convert between Gromacs and NAMD-Charmm formats.
Thank’s for the answer, i will continue search a way to do this.