[gmx-users] Pull code problem: Large fluctuations in pull force in Gromacs 4.5.1 compared to 4.0.5

Dear all, I have a problem using the pull code in Gromacs 4.5.1. I am running simulations with a small molecule at constrained distances from the bilayer center in a membrane (z-direction) in order to calculate permeability data. I use the force acting on the molecule (pullf.xvg) at different

Re: [gmx-users] pull code problem: between protofilaments

Dear Chris, Thank a lot for your reply. I am trying the pull code that you have suggested. And I would be more specific about the problem and code in my future mails. regards, Shilpi On 02/10/11, chris.ne...@utoronto.ca wrote: Dear Shilpi: Can you use something like this? pull  

[gmx-users] pull code problem: between protofilaments

Dear Shilpi: Can you use something like this? pull = umbrella pull_geometry= position pull_dim = N N Y pull_vec1= 0 0 0 pull_start = no pull_ngroups = 1 pull_group0 = PRO-1 pull_pbcatom0

[gmx-users] pull code problem: between protofilaments

Dear Gmx users, I am studying the interaction between the tubulin protofilaments arranged in parallel. For this operation, I have considered a tetramer and a dimer from two protofilaments respectively (say PRO-1 and PRO-2), tetramer in PRO-1 and a dimer in PRO-2. I want to move the dimer of

RE: [gmx-users] pull code problem

. Berk Date: Thu, 6 Aug 2009 10:49:26 +0800 From: djpit...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] pull code problem Hi, all: I tried to pull a specific DPPC, say, r3, out of a pre-equilibrated bilayer into the water along the positive z axis. For the pull code parameters, I used

[gmx-users] pull code problem

Hi, all: I tried to pull a specific DPPC, say, r3, out of a pre-equilibrated bilayer into the water along the positive z axis. For the pull code parameters, I used: pull = umbrella pull_geometry= distance pull_vec1 = 0. 0. 1. pull_dim= N

[gmx-users] pull code problem

hello, I am trying to do a pulling simulation with gromacs 4.0.2 I added the following lines to the .mdp input file for grompp: ... pull = constraint pull_geometry = distance pull_dim = Y Y Y pull_nstxout = 10 pull_nstfout = 10

RE: [gmx-users] pull code problem

] pull code problem hello, I am trying to do a pulling simulation with gromacs 4.0.2 I added the following lines to the .mdp input file for grompp: ... pull = constraint pull_geometry = distance pull_dim = Y Y Y pull_nstxout = 10

[gmx-users] pull code problem

Hi Berk, thank you for the reply here is my mdp file: ; ; User aneamtu ; Joi, 7 mai - 2009 ; Input file ; title = Production_runs ;define = -DPOSRES -DPOSRES_CA2+_IONS ;constraints = all-bonds integrator

RE: [gmx-users] pull code problem

Hi, Maybe there is an older grompp in your path. Type grompp -h to see which version you are using. And: which grompp to see where it comes from. Berk Date: Mon, 11 May 2009 13:03:07 +0300 From: neamtuand...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] pull code problem Hi

[gmx-users] pull code problem solved..

Sorry it appears that something was wrong with my .mdp file .. Idon't know what ...but I wrote again the pull code lines and the warnings dissapeared. Thank you again, Andrei ___ gmx-users mailing listgmx-users@gromacs.org