Re: [gmx-users] Periodic boundary conditions during the simulation

Boundaries of the box used for visualisation are totally arbitrary, it makes not difference when the various simulations are being performed. Most efficient to simply process it at the end to get the visual representation you want Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamic

[gmx-users] Periodic boundary conditions during the simulation

Hello everybody, I know that due to periodic boundary conditions the molecules move from one side of the box to the other side and moves outside the box. I also know how to use trjconv to solve this problem and I usually do this step at the end of the simulation. However I have noticed that after

Re: [gmx-users] Periodic Boundary Conditions

On 2/10/19 12:26 PM, marzieh gharouni wrote: Hello I want to do noPeriodic Boundary Conditions for my system. Gromacs tutorial has said that it can not be used the center and nojump in one command simultaneously. I would be grateful if you could explain the reasons for it? Both apply transla

[gmx-users] Periodic Boundary Conditions

Hello I want to do noPeriodic Boundary Conditions for my system. Gromacs tutorial has said that it can not be used the center and nojump in one command simultaneously. I would be grateful if you could explain the reasons for it? please see this tutorial http://www.gromacs.org/Documentation/Termino

[gmx-users] periodic boundary conditions

Dear Gromacs developers and usersI have three questions. I appreciate it if you answer them: 1)I am doing MD simulation on a bilayer. The problem I have encounteredis that either I do reimaging on the trajectory using –pbc mol –ur compact ornot, the number of Na ions in each leaflet is shown dif

Re: [gmx-users] periodic boundary conditions

Hi, On Wed, Jul 13, 2016 at 5:50 PM Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Mark, > > Thanks for your reply. > > The 6 around 1 setup is also periodic. > > I understand this. However, we can argue the same for 6-1 system as well. > Right? > Sure, but that's not the point.

Re: [gmx-users] periodic boundary conditions

Any other comment on this? :-) On Wed, Jul 13, 2016 at 9:50 AM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Mark, > > Thanks for your reply. > > The 6 around 1 setup is also periodic. > > I understand this. However, we can argue the same for 6-1 system as well. > Right? > > If

Re: [gmx-users] periodic boundary conditions

Hi Mark, Thanks for your reply. The 6 around 1 setup is also periodic. I understand this. However, we can argue the same for 6-1 system as well. Right? If one edge of this hexagonal deforms, the other side also deforms and in fact we are applying a symmetry to our system. The question is: whic

Re: [gmx-users] periodic boundary conditions

Hi, These are different systems. Your 6-around-1 setup (whether itself hexagonally periodic or not) has degrees of freedom that the single hexagonal cell cannot access. In the latter case, if a wall on one edge of the cell deforms, then the corresponding wall on the far side of the cell has the ma

[gmx-users] periodic boundary conditions

Dear gromacs-users, Doing simulations on lipid HII phase, I came to a question which I could not get happy with my answer. I appreciate your opinion in advance: Imagine you have a cylinder made of lipids with waters only inside the cylinder, which is long enough and can be run for enough time so

Re: [gmx-users] periodic boundary conditions pbc=xyz

Hi Ming Use *-pbc mol* while using trjconv. Anyway it is not another box. Best Regards -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB, INDIA -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posti

Re: [gmx-users] periodic boundary conditions pbc=xyz

: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Sunday, 5 April 2015 7:43 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] periodic boundary conditions pbc=xyz Hi Ming, You have another box in

Re: [gmx-users] periodic boundary conditions pbc=xyz

Hi Ming, You have another box in your (infinite) periodic system? Cheers, Tsjerk On Sun, Apr 5, 2015 at 10:32 AM, Ming Tang wrote: > Dear all, > > I did a simulation using periodic boundary conditions pbc=xyz. It turns > out that the box is defined too small, and some atoms go to another box

[gmx-users] periodic boundary conditions pbc=xyz

Dear all, I did a simulation using periodic boundary conditions pbc=xyz. It turns out that the box is defined too small, and some atoms go to another box. Does this affect the simulation result? If not, how to display the real model (without separation) in VMD? Thanks in advance, Ming -- Groma