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 = 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 = > pull_group1 = PRO-2 > pull_pbcatom1 = > pull_init1 = 0 0 > pull_rate1 = 0 > pull_k1 = 500.0 > pull_nstxout = 500 > pull_nstfout = 500 > > The above is for umbrella sampling. If you want to do continuous pulling, > then: > > pull_start = yes > pull_rate1 = > > ### Also: > > Next time you post, please provide more specifics. For example, I suggested a > .mdp file in specifics to you above and I bet it would have been harder for > you to guess what I meant if I had just told you the general idea instead of > pasting some .mdp options. Likewise, your initial post would have been > clearer it you had copied and pasted the .mdp pull code section that you > tried to use. > > Chris. > > -- original message -- > > > 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 PRO-2 over the tetramer of PRO-1 along the length of > protofilaments in one axis only, keeping the PRO-1 fixed to its original > position. I tried by assuming tetramer as 'reference group' and the > dimer as 'pull group' in pull code but the system crashed. > > I have > succeeded in separating two dimers in Z-axis by using > 'distance' geometry. But this case is quite different, as the pulling is > not face-to-face but rather a sliding movement over another > protofilament. Here, the COM distance between the pull group (dimer of > PRO-2) and reference group (tetramer of PRO-1) first decreases and then > increases while it moves. How can I simulate this operation by using pull > code? > > Thanks, > > best regards, > Shilpi Chaurasia > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface or > send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] pull code problem
Hi, First, please switch to 4.0.5, I have put several fixes in the pull code in the 4.0 minor releases. You did not specify pull_init1, nor pull_start, this means you start pulling at a distance of 0, which means the center of the bilayer. Setting pull_start = yes should fix your 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: pull = umbrella pull_geometry= distance pull_vec1 = 0. 0. 1. pull_dim= N N Y pull_nstxout = 1000 pull_group0 = bilayer pull_group1 = r3_P pull_k1 = 500 pull_rate1 = 0.001;nm/ps integrator = md dt = 0.002 ;ps nsteps = 100 nstcomm = 1 comm_grps = DPP SOL nstxtcout = 100 nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.0 ewald_rtol = 1e-5 optimize_fft= yes tcoupl = Berendsen tau_t = 0.10.1 tc_grps = DPPSOL ref_t = 323323 pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 gen_vel = no gen_temp= 323 gen_seed= 173529 constraints = all-bonds constraint_algorithm= LINCS lincs_order = 4 "r3_P" corresponds to an index file that contains the phophorus group of r3, and "bilayer" corresponds to an index file that contains all the lipids except r3. I'm using GROMACS 4.0.3, but when I looked at the trajectory in VMD, the position of r3 is hardly moved. So what's the right way to pull this specific lipid into the water slab? Thanks. dj _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 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 = md > > dt = 0.001 > > nsteps = 5 > > > > nstcomm= 1 > > nstxout= 1000 > > nstvout= 1000 > > nstfout= 1000 > > nstlog = 500 > nstxtcout = 50 > xtc_grps = Protein_ions > > > nstenergy = 100 > > nstlist= 10 > > ns_type= grid > > > coulombtype= PME > > rlist = 1.0 > > rcoulomb = 1.0 > > rvdw = 1.0 > optimize_fft = yes > > > Tcoupl = v-rescale > > tc-grps = Protein SOL ions > > tau_t = 0.1 0.1 0.1 > > ref_t = 310 310 310 > > > > energygrps = Protein SOL CA2+ NA+ CL- > > > > Pcoupl = berendsen > > Pcoupltype = isotropic > > tau_p = 0.5 > > compressibility= 4.5e-5 > > ref_p = 1.0 > > > > gen_vel= no > > gen_temp = 310.0 > > gen_seed = 173529 > > > > pull = constraint > pull_geometry = distance > pull_dim = Y Y Y > pull_nstxout = 10 > pull_nstfout = 10 > pull_ngroups = 2 > pull_group0= Protein > > pull_group1= CA2+1 > pull_rate1 = 0.3 > > pull_group2= CA2+2 > pull_rate2 = 0.3 > > > I do not understand what I do wrong.. > Should I use a -pi pull.ppa file like in gromacs 3.x ? > > Andrei > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] pull code problem
Hi, Do you have another line with "pull =" somewhere in your mdp file? PS You should switch to Gromacs 4.0.4, since it contains several small bug fixes for the pull code. Berk > Date: Mon, 11 May 2009 12:38:35 +0300 > From: neamtuand...@gmail.com > To: gmx-users@gromacs.org > Subject: [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 > pull_ngroups = 2 > pull_group0= Protein > > pull_group1= CA2+1 > pull_rate1 = 0.3 > > pull_group2= CA2+2 > pull_rate2 = 0.3 > > . > > when I run > > grompp -f production_prm.mdp ...etc. > > it does not recognize the keywords for pulling: > > Ignoring obsolete mdp entry 'title' > > Back Off! I just backed up neutr_RCK_Mthk_solv.04.mdout.mdp to > ./#neutr_RCK_Mthk_solv.04.mdout.mdp.6# > > WARNING 1 [file production_prm.mdp, line unknown]: > Unknown or double left-hand 'pull_geometry' in parameter file > > WARNING 2 [file production_prm.mdp, line unknown]: > Unknown or double left-hand 'pull_dim' in parameter file > > WARNING 3 [file production_prm.mdp, line unknown]: > Unknown or double left-hand 'pull_nstxout' in parameter file > > WARNING 4 [file production_prm.mdp, line unknown]: > Unknown or double left-hand 'pull_nstfout' in parameter file > > WARNING 5 [file production_prm.mdp, line unknown]: > Unknown or double left-hand 'pull_ngroups' in parameter file > > WARNING 6 [file production_prm.mdp, line unknown]: > Unknown or double left-hand 'pull_group0' in parameter file > > WARNING 7 [file production_prm.mdp, line unknown]: > Unknown or double left-hand 'pull_group1' in parameter file > > WARNING 8 [file production_prm.mdp, line unknown]: > Unknown or double left-hand 'pull_rate1' in parameter file > > WARNING 9 [file production_prm.mdp, line unknown]: > Unknown or double left-hand 'pull_group2' in parameter file > > WARNING 10 [file production_prm.mdp, line unknown]: > Unknown or double left-hand 'pull_rate2' in parameter file > > ... > > It appears that grompp doesnot recognize any of these keywords... > > Does anybody can help? > > Thank you > Andrei > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
