# Setting up a virtual site to represent a dummy(=massless) LJ sphere **URL:** \ **Category:** User discussions\ **Tags:** forcefield\ **Created:** [December 20, 2021, 3:14pm UTC](https://gromacs.bioexcel.eu/t/setting-up-a-virtual-site-to-represent-a-dummy-massless-lj-sphere/3334 "2021-12-20T15:14:28Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Valentina](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/valentina/32/725_2.png) [@Valentina](https://gromacs.bioexcel.eu/u/Valentina)\ **Post date:** [December 20, 2021, 3:14pm UTC](https://gromacs.bioexcel.eu/t/setting-up-a-virtual-site-to-represent-a-dummy-massless-lj-sphere/3334/1 "2021-12-20T15:14:28Z")
GROMACS version: 2021.3 GROMACS modification: No Sorry, for this long post, just trying to summarise and link all the concepts, as I am struggling to wrap my head around things. I need to create a repulsive area of a given size, it should be able to move around the simulation box as the system relaxes. I thought I could make use of a dummy/virtual LJ spere with some radius, but w/o mass or charge. Obviously, I need a mass for the MD (=forces), so, honestly, I am confused here. → _ **Am I correct to be using dummies for massless repulsive LJ sphere?** _ My approach is as follows, consulting [manual](https://manual.gromacs.org/current/reference-manual/topologies/parameter-files.html#non-bonded-parameters) obviously: 1. add a particle into `ffnonbonded.itp`: ```auto [atomtypes] ; type atnum mass charge ptype sigma epsilon LJ 0 0.0 0.000 V 0.5 0.001 ; LJ test CG331 6 12.011000 0.000 A 0.365268474438 0.3263520 ; aliphatic C for CH3 CG321 6 12.011000 0.000 A 0.358141284692 0.2343040 ; aliphatic C for CH2 HGA3 1 1.008000 0.000 A 0.238760856462 0.1004160 ; alphatic proton, CH3 HGA2 1 1.008000 0.000 A 0.238760856462 0.1464400 ; alphatic proton, CH2 ``` I declare `ptype` as `V` for the virtual site, as per [Table 10](https://manual.gromacs.org/current/reference-manual/topologies/particle-type.html#tab-ptype): → _ **Am I correct that I need particle to be a virtual site, to be able to have no mass, unlike `A` for an atom?** _ → _ **Do I need to make an entry in `atomtypes.atp`? or is it only for `ptype A`?** _ I am reading [Atom types entry in the manual](https://manual.gromacs.org/current/reference-manual/topologies/particle-type.html#atomtype) and I guess no? 1. make an `LJ.itp` for it: ```auto [moleculetype] ; Name nrexcl LJ 0 [atoms] ; id at type res nr residu name at name cg nr charge 1 LJ 1 LJ LJ 1 0.0 ``` Here, I am relying on the mixing rules of the forcefield, as declared under `forcefield.itp`, for instance, these are CHARMM: ```auto [defaults] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 #include "ffnonbonded.itp" #include "ffbonded.itp" ``` If I do not want to rely on whatever I get from the mixing rules, I need to declare the values myself. As per [Table 13](https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#tab-topfile1), I add `[nonbond_params]` into the `ffnonbonded.itp`, for example: ```auto [nonbond_params] ; i j func sigma epsilon LJ CG331 1 0.5 0.001 ; LJ test LJ CG321 1 0.5 0.001 ; LJ test LJ HGA3 1 0.5 0.001 ; LJ test LJ HGA2 1 0.5 0.001 ; LJ test ``` _Self note_: I do not use `[pairs]` & `[pairtypes]` as those are to modify interactions within the molecule itself, see [Table 13](https://manual.gromacs.org/documentation/2021/reference-manual/topologies/topology-file-formats.html#tab-topfile1). 1. I build a system, for example, for 5 LJ and 20 alkanes in a box my `topology.top` looks like this: ```auto #include "../charmm36.ff/forcefield.itp" #include "./c5h.itp" #include "./LJ.itp" [system] alkane + LJ [molecules] ; Compound #mols C5H 20 LJ 5 ``` Now, I am struggling to understand what is ` [virtual_sites1]` entry is for. In my mind, it was something to deal with the massless dummy? In the manual [Virtual sites](https://manual.gromacs.org/current/reference-manual/topologies/particle-type.html#virtual-sites) it is linked to `type 1` interaction, but no such interaction is shown on the Fig 34 in the [Virtual interaction sites](https://manual.gromacs.org/current/reference-manual/functions/interaction-methods.html#virtualsites). It also seems to involve 2 atoms and falls under intramolecular interactions, [Table 14](https://manual.gromacs.org/documentation/2021/reference-manual/topologies/topology-file-formats.html#tab-topfile2) I guess, all I want to understand is: → _**Do I need to use ` [virtual_sites1]` when introducing a massless dummy LJ?**_ → _ **Is there anything I am missing in my setup?** _ → _**More general Q - If I have a massless atom floating around the box (such as in this example), how are the dynamics of it computed? Would MD only be feasible when there are other real (=with mass) atoms in the box?**_ Thank you for your advice and sorry for such long post! V * * * @mholmboe Michael, I am just tagging you here, since I saw [your earlier post](https://gromacs.bioexcel.eu/t/single-ion-virtual-sites-using-virtual-sites1-in-gromacs-2021/1810) and you may have some insight. My Q is a little different, hence, I thought I’d start a new thread rather than piggyback on yours. ---
**Author:** ![mholmboe](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mholmboe/32/753_2.png) [@mholmboe](https://gromacs.bioexcel.eu/u/mholmboe)\ **Post date:** [January 2, 2022, 1:54pm UTC](https://gromacs.bioexcel.eu/t/setting-up-a-virtual-site-to-represent-a-dummy-massless-lj-sphere/3334/2 "2022-01-02T13:54:37Z")
Im answering since I was tagged, not necessarily meaning I can help you… → _ **Am I correct to be using dummies for massless repulsive LJ sphere?** _ _I’m unsure what exactly what you want to achieve. What would be the benefit of using a massless particle? Seems better to use something with a mass, with or without using position restraints and such, and then use a [nonbond\_params] section. Alternatively, have you considered using (inverted) flat-bottom distance restraints (Fig 30.B)? while using refcoord\_scaling=COM_ [https://manual.gromacs.org/documentation/2021/reference-manual/functions/restraints.html#flat-bottomed-position-restraints](https://manual.gromacs.org/documentation/2021/reference-manual/functions/restraints.html#flat-bottomed-position-restraints) → _ **Am I correct that I need particle to be a virtual site, to be able to have no mass, unlike `A` for an atom?** _ _I would think any virtual site has to have one or more parent/s (constructing atoms). Not sure if virtual sites can be single particles, do not think so. Why not use an actual dummy atom with some mass, and/or position restraints?_ → _ **Do I need to make an entry in `atomtypes.atp` ? or is it only for `ptype A` ?** _ I’m unsure. Try running gmx grompp and then gmx dump with the generated .tpr file, to inspect what mass is used for your dummy particle. → _**Do I need to use `[virtual_sites1]` when introducing a massless dummy LJ?**_ _a virtual\_site1 site will only sit on top of its one constructing/parent atom site, as I understand, which means you need an actual atom anyway._ → _ **Is there anything I am missing in my setup?** _ _I do not think so, but I would not recommend using a massless site or a virtual site._ → _**More general Q - If I have a massless atom floating around the box (such as in this example), how are the dynamics of it computed? Would MD only be feasible when there are other real (=with mass) atoms in the box?**_ _I have not tried, but would assume the actual physics would be unreal since the massless particle might achieve insane velocities? I assume Gromacs would not be happy._ _All the best,_ _Michael Holmboe_