[gmx-users] Molecules in micelles

Dear Gromacs Users, My system contains two micelles. In order to calculate the radius of gyration for two micelles, I need to select molecules in each micelle. Is there any tool available in Gromacs to do that? If available, what options in the -h should I use to get the information I want.

[gmx-users] Commented atoms in [pair] list

Dear Gromacs users, Recently, I downloaded some simulation files from a web site (their work is already published). Once I checked their itp files, I saw that they commented some atoms in [pair] list. I would like to know what could be the reason for that? Thank you.  -- Gromacs Users mailing

[gmx-users] How to get the complete molecule?

Dear All, In my simulation, part of my molecule is in a one cell and the other part is in the adjacent cell. I want to get the complete molecule in the pdb format in the center of the box. I tried to do that using gmx trjconv -f run.pdb -s run.tpr -pbc mol -ur compact -center -o run_new.pdbBut

[gmx-users] Hexagonal Phase modelling

Dear Gromacs users, I want to model a hexagonal phase and do  MD simulations using gromacs. Could you please guide me to model a hexagoanl phase for my CiEj molecules? Thank you. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] spc.itp file and flexspc.itp

- This repositery contains files to simulate CiEj surfactants using the GROMOS-compatible 2016H66 f... | | | On Monday, 4 June 2018, 10:05:12 pm AEST, Justin Lemkul wrote: On 6/4/18 6:13 AM, Anjana Jayasinghe wrote: > Dear Gromacs Users, > Is there any difference in the simu

[gmx-users] spc.itp file and flexspc.itp

Dear Gromacs Users, Is there any difference in the simulation, if we define the spc.itp as, | #ifdef FLEX_SPC | | | #include "flexspc.itp" | | | #else | | | #include "spc.itp" | | | #endif | instead of using the single line  #include "spc.itp" ? Can anyone help me to understand the

[gmx-users] MD simulation error

Dear Gromacs users, If I am not getting the expecting (experimental) behavoir of my system using MD simulations, what could be the best option to do with MD simulations? Thank you. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Trans Dihedral Fraction

Dear Gromacs users, I tried to calculate fraction of trans dihedrals in my molecule using gmx angle -f traj.xtc -of -n dihedral.ndx -type dihedral However, I couldn't get dihfrac.xvg output file from -of option. What is the reason for this. Can anyone help me? Thank you. -- Gromacs Users

[gmx-users] Fraction of trans dihedrals

Dear Gromacs Users, Is there any method of using gmx angle to get a fraction of trans dihedrals? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Dihedral Angle Distribution

Lemkul <jalem...@vt.edu> wrote: On 4/16/18 3:07 AM, Anjana Jayasinghe wrote: > Dear Gromacs Users, > I want to calculate dihedral angle distribution for 9 dihedral angles in > aliphatic chain of my molecule. I created the index file giving the command > make_ndx -f run.gro -

[gmx-users] Dihedral Angle Distribution

Dear Gromacs Users, I want to calculate dihedral angle distribution for 9 dihedral angles in aliphatic chain of my molecule. I created the index file giving the command make_ndx -f run.gro -o dihedral.ndxThen  I typed,a C13 a C14 a C15 a C16a C14 a C15 a C16 a C17a C15 a C16 a C17 a C18a C16 a

[gmx-users] Keeping cis configuration of a molecule

Dear All, I want to keep the cis configuration of my molecule in MD simulation. How can I do that? Could you please help me? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] 2016H66 force field

Dear All, I would like to know that do we need to change bond lengths and bond angles such as gb_1, gb_18, ga_12 and ga_15 (according to OXY) for MD simulations of CiEj or PEO molecules when we use 2016H66 force field? Thank you. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Dihedral parameters in Gromos53A6OXY+D

Dear All, I am trying to change the parameters for a PEG molecule using OXY+D ( https://pubs.acs.org/doi/abs/10.1021/ct300245h) parameters. When I tried to change the dihedral angles of C-C-O-C and O-C-C-O,  there are three new defined dihedral angles for each mentioned types. But in original

Re: [gmx-users] Non bonded parameters

ul <jalem...@vt.edu> wrote: On 12/28/17 4:24 PM, Anjana Jayasinghe wrote: > Dear All, > If I change (I want to use non-boned parameters defined in a published > article) the single atom Lennard-Jones interactions parameters (C6 and C12 > present in [atomtypes] of ffnonbonded

[gmx-users] Non bonded parameters

help me? Thank you. Sincerely,Anjana Jayasinghe -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https