Re: [gmx-users] AFM pulling simulations

X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks,

Re: [gmx-users] AFM pulling simulations

http://www.gromacs.org/Documentation/Tutorials On 03/22/2011 11:02 AM, X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these

RE: [gmx-users] AFM pulling simulations

apply the force in that direction). Date: Tue, 22 Mar 2011 11:15:54 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] AFM pulling simulations X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations

RE: [gmx-users] AFM pulling simulations

too eager to send an email.. I think playing with editconf with princ flag should do the trick .. sorry folks and thanks for the help !! From: xru...@live.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] AFM pulling simulations Date: Tue, 22 Mar 2011 15:47:41 + Thanks

Re: [gmx-users] AFM Pulling Simulations

On 26/08/10 19:56, chris.ne...@utoronto.ca wrote: Natalie: It would also be a good idea for you to ensure that your supervisor knows how difficult it is to learn and correctly apply these methods. If they think that a person can learn linux and gromacs and the gromacs pull code in a short

Re: [gmx-users] AFM Pulling Simulations

Natalie Stephenson wrote: Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few problems!! I've managed to perform all the

Re: [gmx-users] AFM Pulling Simulations

Quoting Justin A. Lemkul jalem...@vt.edu: Natalie Stephenson wrote: Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few

RE: [gmx-users] AFM pulling rate

Hi, The pull code in Gromacs 3 is pretty messy. The rate is in nm/ps. The force is (unfortunately) not written to the pdo file. You have to redetermine it from the positions, but beware that one of the two groups could jump over the periodic boundary. In Gromacs 4 (and the current CVS) I have

RE: [gmx-users] AFM Pulling and com motion

From: Zhou Bo [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: RE: [gmx-users] AFM Pulling and com motion Date: Fri, 21 Sep 2007 00:49:21 +0800 Thanks for your reply. There is no absolute reference here. The system

RE: [gmx-users] AFM Pulling and com motion

From: Zhou Bo [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] AFM Pulling and com motion Date: Thu, 20 Sep 2007 11:06:09 +0800 Hi GXM Users, I'm trying to execute some AFM Pulling. I followed the pull

RE: [gmx-users] AFM Pulling and com motion

Thanks to Berk. I just tested two system, one with stopcm and the other without stopcm. I calculated the pull forces and compared them with each other. There are really some distinct differences between them during the 80ps simulation. I worry about it, for example, in long time simulations, so

RE: [gmx-users] AFM Pulling and com motion

You didn't tell if you are using an absolute reference or not. With an absolute reference you should not remove the com motion. Berk. From: Zhou Bo [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: RE: [gmx-users] AFM

RE: [gmx-users] AFM Pulling and com motion

for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: RE: [gmx-users] AFM Pulling and com motion Date: Thu, 20 Sep 2007 22:44:29 +0800 Thanks to Berk. I just tested two system, one with stopcm and the other without stopcm. I calculated the pull forces and compared them with each

Re: [gmx-users] AFM Pulling

Hi all, nevermind, I caught my own mistake. (I hope this might be useful for someone in the future). PeptidePull.ppa is my input file, specifying the parameters for my pulling. -po PeptidePull is the output file. The problem here is that I used the same name. When it crossed over to

RE: [gmx-users] AFM pulling

From: Susanna Hug [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] AFM pulling Date: Mon, 14 Aug 2006 13:23:28 +0200 Hi gmx-users! I am trying to simulate the diffusion of mannitol through a lipid bilayer

RE: [gmx-users] AFM pulling

Thanks, that's good to know! Susanna From: Susanna Hug [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] AFM pulling Date: Mon, 14 Aug 2006 13:23:28 +0200 Hi gmx-users! I am trying to simulate the

Re: [gmx-users] AFM Pulling Rate

Hello Bob, have you tried to define the initial position of the AFM-tip? It needs to be set to the position of the COM of the group you want to pull. try and add afm_init1 = x y z (x y z = position where the afm should be) to your pull.ppa. Otherwise your afmspring is extended from the

Re: [gmx-users] afm pulling and comm_mode

Hi again, I pretty much went about the setting up of afm pulling calculations. Still I am a little bit concern about the results. When using gmx3.2.1 and applying a Linear removal of the center of mass (i.e. translation) I see the cell unit still moving during the simulation in a direction

Re: [gmx-users] afm pulling

Hi There seems to be something wrong with your init-vector. Ich have written a small python script, which simply calculates the vector for convenience purposes. You still need the pull- and COM-group coordinates, though. But that shouldn't be a problem. If you want it, I'll send it via mail.

Re: [gmx-users] afm pulling

Thanks Emily and Maik for your feed-back You both are right regarding the init vector. I happened to be the sign of it as Emily guessed. Changing the direction by doing xpull-xref, ypull -yref, zpull-zref and not xref-xpull.works fine. Thanks for the offer on the script though. Thanks

Re: [gmx-users] afm pulling

Emily Walton wrote: afm_init describes only the initial position of the spring. afm_dir describes how that position will change with time. You can normalize afm_init and use it for afm_dir if you want- you'd be pulling along the direction connecting the com of your reference and pull

Re: [gmx-users] afm pulling

Hi, Dear all, I am simulating an unbinding process with the pull code (afm option). I've been reading previous posts about this option and I just wanted to clarify some ideas and ask some questions. There are: 1-The pulling can be done choosing two different molecules. Why a particular group