[gmx-users] gmx wheel

Hello, I am trying to create a helical wheel. The format of .dat file is: No. of residues Names of the residues But it is giving error: Incorrect usage of option -f Can anyone help me with correct format ? Regards, Amit Behera -- This message has been scanned for viruses and dangerous

[gmx-users] Heme lost

Hello everyone,                      I am using FF: 43a1Spc water modelversion:5.0.7 I was preparing system of protein containing heme and generated pdb at 1ns. But when I observed the pbd, heme group was lost but protein was present there. Kindly help me out. Suggest me some solution.         

Re: [gmx-users] Adding water to specific part of a box

Thanks Victor! - Original Message - From: "Victor Rosas Garcia" To: gmx-us...@gromacs.org Sent: Monday, February 13, 2017 9:30:12 PM Subject: Re: [gmx-users] Adding water to specific part of a box You could try resizing the box of your system with gmx editconf,

[gmx-users] Simulated Tempering in Gromacs 5

Dear all, I was trying to run a Simulated Tempering simulation with Gromacs 5.0.7. After adding the following parameters to the mdp file, I got Segmentation fault after grompp: """ simulated-tempering = yes sim-temp-low = 310 sim-temp-high = 350 simulated-tempering-scaling = linear

Re: [gmx-users] Creating an FCC lattice surface in GROMACS

There isn't, even if we assume that Gromacs is the right tool for the job. Periodic structures are elementary to generate with scripts. Of much more concern is the fact that you may be trying to model a metal surface as a collection of van der Waals particles. Alex On Mon, Feb 13, 2017 at 5:43

[gmx-users] Creating an FCC lattice surface in GROMACS

Hi, I need to create a tethered FCC lattice surface in GROMACS. Is there any way of doing this directly in GROMACS? Is there any other software that can be used for the same and imported into GROMACS? Thanks! Raj. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] How to calculate the angle between the bilayer normal and the P−N vector?

Dear gromacs users, I need to calculate the angle between the bilayer normal and the P−N vector. Gathering information (but I'm not sure), I think one way to do this is: 1- Generate an index.ndx with g_selection of all the P and N of a monolayer. 2- Then use g_bundle as follows: g_bundle

[gmx-users] Polymer Simulations

hii For polymer simulations, what parameters to calculate to check whether the simulations is correct or not..? Which are the main common parameters to calculate for polymer simulations? Regards -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] run parameters

Thank You Sir for your answer. On Fri, Feb 10, 2017 at 5:50 PM, Erik Marklund wrote: > Dear Nikhil, > > It depends, but generally no electrostatic cut-offs since there is no > dielectric medium, making the effective range of electrostatics very long. > And no pbc. If

Re: [gmx-users] Adding water to specific part of a box

I mean adding water above the membrane bilayer and not below it for example. There is an option in VMD in Selection part, which allows the user remove water molecules from z>(upper bond) and z<(lower bond), but I don't know if there is any option which allows you insert water molecules like

Re: [gmx-users] Adding water to specific part of a box

What do you mean by "specif part"? For example just in binding site of protein-ligand and not in other part? On Mon, Feb 13, 2017 at 5:02 PM, Neda Rafiee wrote: > Dear users, > Any one knows how to add water molecules only to specific parts of a > system in GROMACS? > -- >

[gmx-users] Adding water to specific part of a box

Dear users, Any one knows how to add water molecules only to specific parts of a system in GROMACS? -- 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] Topology for oxygen

Hi members,          I am new to gromacs. I want to generate oxygen topology manually for my hemoglobin protein. Can anyone please guide me how we manually generate topology ? what are the steps included?