[gmx-users] Issuing multiple commands simultaneously

I have a series of commands which I want to run a simulation. Is there a way I can issue them together at the start such that the second command is automatically executed after the first one finishes and so on without any manual input. Thanks in advance. -- gmx-users mailing list

[gmx-users] Re:Applying periodic boundary conditions in energy minimization

,then Gromacs will run successfuly afterwards. At 2013-04-03 22:51:54,Abhinav Agrawal abhv.a...@gmail.com wrote: Hi, I have a polymer box on which I wish to apply energy minimization. However, when I do energy minimization runs to polymer chain unravels and goes out of the box. I guess

[gmx-users] Re: Re: Re: Applying periodic boundary conditions in energy minimization

...@vt.edu Subject: Re: [gmx-users] Re: Applying periodic boundary conditions in energy minimization To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 515d3681.30...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/3/13 9:46 PM, Abhinav

[gmx-users] Applying periodic boundary conditions in energy minimization

Hi, I have a polymer box on which I wish to apply energy minimization. However, when I do energy minimization runs to polymer chain unravels and goes out of the box. I guess this is because periodic conditions are not applied. My em.mdp file is: ; cpp = /usr/bin/cpp define

[gmx-users] Using two integrators in energy minimization

I want to use both steepest descent and conjugate gradient in my energy minimization. I need the system to use steepest descent for a given number of steps and then switch over to conjugate gradient. Can anyone please suggest how I can do this? How should I make the em.mdp file Thanks in

[gmx-users] Re: Applying periodic boundary conditions in energy minimization

Hi, I have a polymer box on which I wish to apply energy minimization. However, when I do energy minimization runs to polymer chain unravels and goes out of the box. I guess this is because periodic conditions are not applied. My em.mdp file is: ; cpp =

[gmx-users] Making composite box in gromacs

I have polymer and clay structures and I need to study their surface interaction. How do I keep a clay box on top of polymer. Thanks in advance. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] Re: gmx-users Digest, Vol 107, Issue 133

composite box in gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 5158203e.3020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 3/31/13 6:38 AM, Abhinav Agrawal wrote: I have polymer and clay structures and I need to study their surface