[gmx-users] (no subject)

Hello all, I modeled a hexagonal box of water using the following steps: gmx solvate -cs spc216.gro -o waterst1 -box 6 6 6 gmx editconf -f waterst1.gro -o w120.gro -bt tric -box 4.5 4.5 5.56 -angles 90 90 120 -c After which i used trjconv with -pbc atom -ur compact and obtained the hexagonal

[gmx-users] multiple ion species in a single structure.

dear all I am struggling to understand why I cannot add several ion species into one structure. I want certain numbers of K CL NA ions. I use the following commands: gmx genion -s ions.tpr -o x_solv_ions.gro -p topol.top -pname K -nname CL -nn 3 -np 2 gmx genion -s ions.tpr -o

Re: [gmx-users] (no subject)

Hi, I don't know whether solvate supports such boxes, but if it does I would use editconf first to describe the box, and then solvate to fill it. Currently you are filling a cubic box and then transforming it to another shape, and that isn't a well formed operation. Mark On Mon, May 14, 2018 at

Re: [gmx-users] multiple ion species in a single structure.

Hi, If you're doing an operation in stages, then the output of the first phase needs to contribute to the input for the second, e.g. make a new tpr. Otherwise, we'll need more information about what output you got and why it didn't match your expectations. Mark On Mon, May 14, 2018, 10:57 Anna

Re: [gmx-users] multiple ion species in a single structure.

Not sure if this got sent (I received a weird 'server busy' message here), but see below. On 5/14/2018 3:06 AM, Alex wrote: Hi Anna, Indeed, genion requires the tpr generated with the previous set of ions to add new species, so your approach won't work. Here's what routinely works for me

Re: [gmx-users] free energy landscape

Sounds like a problem for string methods. However, it's hard to judge without actually looking at what you have. Cheers. On Sun, May 13, 2018 at 3:47 PM Rezgar Pakravan wrote: > ​HI there > > I got free energy landscape using Mathematica software to get coordinates >

Re: [gmx-users] Problem with gmx clustsize ..(Not enough memory. Failed to calloc)

Hi, Clustering requires that you build a matrix in memory that contains the difference between each structure you intend to cluster. If you e.g. use every frame from your trajectory, then you will typically exhaust the available memory, as here. Reconsider how you will find out the period between

[gmx-users] Problem with gmx clustsize ..(Not enough memory. Failed to calloc)

Thank you Mark for your answer! I have also tried to run clustsize using different dt, from 1 ns to 10ns (the trajectory only have 10 frames) but it still give the same error, so I think that I am doing something wrong. May be the problem is the way the program identify each molecule. Thank you

[gmx-users] Solvating a non-orthogonal box

Hi I have a box whose vectors are given by: (7.972620.0 0.0), (-0.96054 2.33646 0.0), (15.0 0.0 0.0). I would like to fill this box with water. When I use gmx solvate to fill this box, it seems to be introducing a rectangular shaped box of water,

Re: [gmx-users] Problem with gmx clustsize ..(Not enough memory. Failed to calloc)

Den 2018-05-14 kl. 12:40, skrev Sergio Garay: Thank you Mark for your answer! I have also tried to run clustsize using different dt, from 1 ns to 10ns (the trajectory only have 10 frames) but it still give the same error, so I think that I am doing something wrong. May be the problem is the way

Re: [gmx-users] Solvating a non-orthogonal box

This isn't a PBC issue with visualising the box, is it? Turn on the neighbouring images when visualising, and you will be able to see quickly if the entire space is actually filled or not. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical

Re: [gmx-users] Final structure broken

On 5/14/18 8:42 PM, Dhumal, Nilesh wrote: Hello Users, I am running simulation for 1-hexyl-3-methylimidazolium chloride ionic liquid using GROMACS - 2018.1. Simulation box have 128 ion pairs. Initial conformation was minimized and later performed NVT and NPT simulation (1.25ns )at 400K

Re: [gmx-users] Final structure broken

On 5/14/18 8:52 PM, Dhumal, Nilesh wrote: Just for curiosity, Why it is not broken at 400 K? I didn't see similar results for other system also. I did simulation for 800 water molecules using same mdp file, the final structure was not broken. Maybe every atom just happened to be within the

[gmx-users] Final structure broken

Hello Users, I am running simulation for 1-hexyl-3-methylimidazolium chloride ionic liquid using GROMACS - 2018.1. Simulation box have 128 ion pairs. Initial conformation was minimized and later performed NVT and NPT simulation (1.25ns )at 400K respectively. gmx grompp -f nvt_equ_400.mdp -c

Re: [gmx-users] Final structure broken

Just for curiosity, Why it is not broken at 400 K? I didn't see similar results for other system also. I did simulation for 800 water molecules using same mdp file, the final structure was not broken. Nilesh From: Dhumal, Nilesh Sent: Monday, May 14, 2018

[gmx-users] gmx potential

Dear Justin,I used gmx potential command to obtained electrostatic potential across the DPPE membrane. I think my finding isn't true because there is a peak at the center of bilayer and in the head group there are two maximum that are small and mild in the head group. In the same case for DPPC,