Re: [gmx-users] Neutralizing

Dear Sir Use this command: gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral In this case, you don't need ​the number of ions​. Kind Regards Parham J. K. ** *​​* *==* *​==​* *=* ​PhD candidate - Lecturer in drug discovery Faculty of Medicine and Health

[gmx-users] Neutralizing

Hi everybody, I’ve generated a water-peptide system, now I want to neutralize it. Is adding adequate number of ions sufficient for neutralizing process or I should do QM/MM simulation for the this process? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] query on plotting dynamical quantity

Hi Jagannath, Convert the file to PDB format and write the values to the b-factor field. Most visualization programs can color by b-value. Cheers, Tsjerk On Mar 8, 2016 06:50, "Jagannath Mondal" wrote: > Dear gromacs-users > > I am sorry to write you a

[gmx-users] query on plotting dynamical quantity

Dear gromacs-users I am sorry to write you a visualization-related query. I hope you can help. My query is: How can I visualize a trajectory file ( example in vmd) where I have an extra 4th column ( apart from x y z which are first 3 columns) which has a dynamically changing variable for each

[gmx-users] distance restraints in mdp

i am performing protein ligand binding free energy calculation MD. i have applied distance restraint to 1 pair of atoms. now when i am running md it gives me LINCS warnings. first i thought it is because of wrong geometry so i changed complex, now i am doing it for Lysozyme+JZ4. but still same

[gmx-users] TIP5P and crystal waters

Hi, I am trying to run a simulation with TIP5P and Gromacs 5.1.2. I want to do so by keeping the crystal waters in the .pdb file. When I don’t erase the crystal waters and run pdb2gmx, I get the following error: Fatal error: Residue 'HO5' not found in residue topology database This error

[gmx-users] Regression test 4.6.7

Dear all, I am looking for the file regressiontests-4.6.7.tar.gz. I can't find it online, the previous links are done. Can someone please either send it to me or tell me where to find it? Thanks a lot. Nicolas -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] problem with water models in Gromacs 5.1.2

Hi, Yes, the tests were performed. It turns out that I had to reduce the energy step size during minimization. Thank you. Best, Irem > On Mar 6, 2016, at 11:27 AM, Justin Lemkul wrote: > > > > On 3/4/16 4:04 PM, Irem Altan wrote: >> Hi, >> >> It turns out that my problems

Re: [gmx-users] Regarding error while generating topology for protein

On 3/7/16 6:31 AM, shrikant kaushik wrote: hello sir, I have query related to topology file generation for my protein, THR residue is Phosphorylated (TPO), it showing error while running pdbtogmx. how to generate topology file for protein along with TPO residue.

Re: [gmx-users] Extending the simulation

Yes I have done it now. Thank you so much guys.  Sent from my iPhone > On 07-Mar-2016, at 4:32 pm, jkrie...@mrc-lmb.cam.ac.uk wrote: > > This page is now a little out of date. GROMACS 5 has replaced tbpconv with > gmx convert-tpr but otherwise the instructions are the same. > >>

Re: [gmx-users] GROMOS force field for sphingomyelin and cholesterol

You need to be a bit more specific. What other lipids do you have in the membrane and which force field are you/do you want to use for these (and I mean more than just GROMOS, but exactly which parameters they are e.g. 43A1-S3, 53A6L, etc.). There are some GROMOS compatible force fields out

Re: [gmx-users] Extending the simulation

This page is now a little out of date. GROMACS 5 has replaced tbpconv with gmx convert-tpr but otherwise the instructions are the same. > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations > > -- > Gromacs Users mailing list > > * Please search the archive at >

Re: [gmx-users] Extending the simulation

Thank you very much. Regards Suniba On Mon, Mar 7, 2016 at 10:09 AM, Nikhil Maroli wrote: > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations > > -- > Gromacs Users mailing list > > * Please search the archive at >