[gmx-users] Re: Pulling

2013-06-30 Thread Thomas Schlesier
If you use periodic boundary conditions, there is no need that the protein stays at one side of the box. For the pulling simulation: Read the chapters 6.4 (explains the pull-code) and 7.3.21 (explains the mdp-paramters). Additional information you an also get from Justin Tutorial for Umbrella Sa

Re: [gmx-users] Re: Pulling ion - US

2012-12-12 Thread Steven Neumann
Thank you all! On Tue, Dec 11, 2012 at 12:54 PM, Leandro Bortot wrote: > I have made SMD simulations in order to separate a Ca2+ ion from its > complexation site in the protein, which had charge of about -6 e. Without > position constraints in the protein alpha carbons it unfolded in every

Re: [gmx-users] Re: Pulling ion - US

2012-12-11 Thread Leandro Bortot
I have made SMD simulations in order to separate a Ca2+ ion from its complexation site in the protein, which had charge of about -6 e. Without position constraints in the protein alpha carbons it unfolded in every pull simulation. 2012/12/11 Thomas Schlesier > wont happen, since the prob

[gmx-users] Re: Pulling ion - US

2012-12-11 Thread Thomas Schlesier
I would also use the same residue from the pulling for the US. One thing you should be aware of is the pulling dimension: Now you have the pull-code only ativated for the z-direction. If you use this still in the US the ion can move freely in the xy-plane (freely in the sense of what is possible

[gmx-users] Re: pulling simulation using implicit solvent in GROMACS

2010-08-10 Thread Justin A. Lemkul
Please keep all Gromacs-related correspondence on the gmx-users list. Implicit solvent is available in the current 4.5 beta release. Another tip: the mailing list search would have turned this same answer up in a few seconds. This same question has been asked dozens of times. -Justin Samra

RE: [gmx-users] Re: pulling

2009-08-05 Thread Berk Hess
You really need pull_pbcatom0, since your slab is thicker than half the box you otherwise can have periodicity errors. Berk > Date: Wed, 5 Aug 2009 15:27:06 +0200 > From: alexander.h...@mytum.de > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Re: pulling >

Re: [gmx-users] Re: pulling

2009-08-05 Thread aherz
m0). Thx, Alex Berk Hess schrieb: > No (completely) frozen groups are treated correctly. > I had to look in (my own) code again, but for a fully frozen group > the inverse mass is set to 0 in the pull code. > > Berk > > > Date: Fri, 31 Jul 2009 12:49:55 +0200 > > Fro

RE: [gmx-users] Re: pulling

2009-07-31 Thread Berk Hess
No (completely) frozen groups are treated correctly. I had to look in (my own) code again, but for a fully frozen group the inverse mass is set to 0 in the pull code. Berk > Date: Fri, 31 Jul 2009 12:49:55 +0200 > From: schl...@uni-mainz.de > To: gmx-users@gromacs.org > Subject: [g

[gmx-users] Re: pulling

2009-07-31 Thread Thomas Schlesier
Could it also be possible that 'pull = distance' makes problems because it pulls both groups and here one group is frozen? Only an idea, i have never tried to pull a frozen molecule. Thomas > -- > > Message: 5 > Date: Fri, 31 Jul 2009 12:38:19 +0200 > From: Berk Hess

RE: [gmx-users] Re: Pulling a CG protein

2009-07-31 Thread Berk Hess
vector between the two COM's. Berk > Date: Fri, 31 Jul 2009 09:58:56 +0200 > From: schl...@uni-mainz.de > To: gmx-users@gromacs.org > Subject: [gmx-users] Re: Pulling a CG protein > > Hi Johnny, > i replied something to the pull-code of your question. But problem was, >

[gmx-users] Re: Pulling a CG protein

2009-07-31 Thread Thomas Schlesier
Hi Johnny, i replied something to the pull-code of your question. But problem was, i didn't edited the subject line... So here is my answer (see below) with the right subject line (so that you hopefully find it). Hope it helps you. Thomas > > Message: 3 > Date: Thu, 30 Jul 2009 12:08:40 -0700 (PD