Re: [gmx-users] pull code absolute reference
bv07ay wrote: Hello, i am having trouble using the pull options in gromacs 4.0.4. i am simply trying to move a protein from the top of the box to a certain point in the center. i have had no luck using a constant pulling or umbrella pulling the error i receive is: "You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts." here is my most recent .mdp pull options: ; PULL pull= umbrella pull_geometry= position ;pull_group0= pull_init1= 3.279 3.279 3.90 pull_group1= MID pull_dim= Y Y Y pull_k1= 50 is there a way to make my system have an absolute reference? or is there some other way of pulling it that has worked for others? The error message is related less to the pull options than it is to COM motion removal. For instance: http://lists.gromacs.org/pipermail/gmx-users/2009-April/041329.html http://lists.gromacs.org/pipermail/gmx-users/2006-July/022753.html If you search the mailing list archives you will find lots of related posts. I pulled those up immediately by searching: "absolute reference" pulling. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
[gmx-users] pull code absolute reference
Hello, i am having trouble using the pull options in gromacs 4.0.4. i am simply trying to move a protein from the top of the box to a certain point in the center. i have had no luck using a constant pulling or umbrella pulling the error i receive is: "You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts." here is my most recent .mdp pull options: ; PULL pull= umbrella pull_geometry= position ;pull_group0= pull_init1= 3.279 3.279 3.90 pull_group1= MID pull_dim= Y Y Y pull_k1= 50 is there a way to make my system have an absolute reference? or is there some other way of pulling it that has worked for others? -- 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
[gmx-users] pull code absolute reference artifacts
Thanks for the explanation Berk, I am simply trying to do some tests to ensure that the pull code and free energy code are working properly in combination. For this I tried to simplify my 'problem' and apply double-decoupling to a solute in a box of water under 2 conditions: 1) no pull code, and 2) pull code with an absolute reference to pin the decoupled molecule in place harmonically. Since the water box is isotropic, I should get the same overall free energy for decoupling (which I do in spite of the warning message, perhaps because I don't change the reference position over time). Thanks again, Chris. -- original message -- Hi, I have no clue why you would want to fix the peptide in the middle of the box. But what you want seems to be more like com removal for the peptide only with the comm options. The pull code will do approximately what you want, but with pressure coupling there is the problem that your peptide will stay fixed in space, while the rest of the system has to scale around it. In general there are problems with absolute reference pulling, because you just fix the location of the pull group, whereas the rest of the system can freely move, thus the net effect is zero, except for lots of nasty artifacts when you change the pull position too fast. Berk Date: Thu, 16 Apr 2009 10:27:04 -0400 From: chris.neale at utoronto.ca To: gmx-users at gromacs.org Subject: [gmx-users] pull code absolute reference artifacts Hello, I have a question about the following grompp 4.0.4 warning: "You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts." While I do realize that this is an excellent error message containing lots of information, I am still unclear about how to proceed. Why does my system not have an absolute reference? Is it because I have pbc and center of mass motion removal? Exactly what types of artifacts are expected? Is there a simple solution? I am trying to hold my peptide in the center of a water box. I realize that there is no "center" and everything in pbc, but I need to do it nevertheless. Here are my .mdp options: pull= umbrella pull_geometry = distance pull_dim= Y Y Y pull_ngroups= 1 ;pull_group0 = pull_group1 = peptide_A pull_k1 = 500 pull_init1 = 0.00 nsteps = 25 ; REMOVE_FOR_EM tinit = 49000 ; REMOVE_FOR_EM dt = 0.004 ; REMOVE_FOR_EM nstxout = 25 ; REMOVE_FOR_EM nstvout = 25 ; REMOVE_FOR_EM nstfout = 25 ; REMOVE_FOR_EM nstenergy = 25000 ; REMOVE_FOR_EM nstxtcout = 25000 ; REMOVE_FOR_EM nstlog = 25; REMOVE_FOR_EM gen_vel = no unconstrained-start = yes integrator = sd gen_seed= -1 comm_mode = linear nstcomm = 1 comm_grps = System nstlist = 5 ns_type = grid pbc = xyz coulombtype = PME rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 vdwtype = cut-off rvdw_switch = 0 rvdw= 1.4 rlist = 0.9 DispCorr= EnerPres Pcoupl = Berendsen ; REMOVE_FOR_EM pcoupltype = isotropic ; REMOVE_FOR_EM compressibility = 4.5e-5 ; REMOVE_FOR_EM ref_p = 1. ; REMOVE_FOR_EM tau_p = 4.0; REMOVE_FOR_EM tc_grps = System ; REMOVE_FOR_EM tau_t = 1.0; REMOVE_FOR_EM ld_seed = -1 ; REMOVE_FOR_EM ref_t = 300. ; REMOVE_FOR_EM gen_temp= 300. ; REMOVE_FOR_EM constraints = all-bonds ; REMOVE_FOR_EM constraint_algorithm= lincs ; REMOVE_FOR_EM lincs-iter = 1 ; REMOVE_FOR_EM lincs-order = 6 ; REMOVE_FOR_EM ___ gmx-users mailing listgmx-users at 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-request at 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/ -- next part ---
RE: [gmx-users] pull code absolute reference artifacts
Hi, I have no clue why you would want to fix the peptide in the middle of the box. But what you want seems to be more like com removal for the peptide only with the comm options. The pull code will do approximately what you want, but with pressure coupling there is the problem that your peptide will stay fixed in space, while the rest of the system has to scale around it. In general there are problems with absolute reference pulling, because you just fix the location of the pull group, whereas the rest of the system can freely move, thus the net effect is zero, except for lots of nasty artifacts when you change the pull position too fast. Berk > Date: Thu, 16 Apr 2009 10:27:04 -0400 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] pull code absolute reference artifacts > > Hello, > > I have a question about the following grompp 4.0.4 warning: > > "You are using an absolute reference for pulling, but the rest of the > system does not have an absolute reference. This will lead to > artifacts." > > While I do realize that this is an excellent error message containing > lots of information, I am still unclear about how to proceed. Why does > my system not have an absolute reference? Is it because I have pbc and > center of mass motion removal? Exactly what types of artifacts are > expected? Is there a simple solution? > > I am trying to hold my peptide in the center of a water box. I realize > that there is no "center" and everything in pbc, but I need to do it > nevertheless. > > Here are my .mdp options: > > pull= umbrella > pull_geometry = distance > pull_dim= Y Y Y > pull_ngroups= 1 > ;pull_group0 = > pull_group1 = peptide_A > pull_k1 = 500 > pull_init1 = 0.00 > > nsteps = 25 ; REMOVE_FOR_EM > tinit = 49000 ; REMOVE_FOR_EM > dt = 0.004 ; REMOVE_FOR_EM > nstxout = 25 ; REMOVE_FOR_EM > nstvout = 25 ; REMOVE_FOR_EM > nstfout = 25 ; REMOVE_FOR_EM > nstenergy = 25000 ; REMOVE_FOR_EM > nstxtcout = 25000 ; REMOVE_FOR_EM > nstlog = 25; REMOVE_FOR_EM > gen_vel = no > unconstrained-start = yes > > integrator = sd > gen_seed= -1 > comm_mode = linear > nstcomm = 1 > comm_grps = System > nstlist = 5 > ns_type = grid > pbc = xyz > coulombtype = PME > rcoulomb= 0.9 > fourierspacing = 0.12 > pme_order = 4 > vdwtype = cut-off > rvdw_switch = 0 > rvdw= 1.4 > rlist = 0.9 > DispCorr= EnerPres > Pcoupl = Berendsen ; REMOVE_FOR_EM > pcoupltype = isotropic ; REMOVE_FOR_EM > compressibility = 4.5e-5 ; REMOVE_FOR_EM > ref_p = 1. ; REMOVE_FOR_EM > tau_p = 4.0; REMOVE_FOR_EM > tc_grps = System ; REMOVE_FOR_EM > tau_t = 1.0; REMOVE_FOR_EM > ld_seed = -1 ; REMOVE_FOR_EM > ref_t = 300. ; REMOVE_FOR_EM > gen_temp= 300. ; REMOVE_FOR_EM > constraints = all-bonds ; REMOVE_FOR_EM > constraint_algorithm= lincs ; REMOVE_FOR_EM > lincs-iter = 1 ; REMOVE_FOR_EM > lincs-order = 6 ; REMOVE_FOR_EM > > > ___ > 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
Re: [gmx-users] pull code absolute reference artifacts
Hi Justin: 1) EXTREMELY IMPORTANT: I already know of 1 person, but is anyone alergic to either Iodine or Chlorine? No, I am not alergic to those compounds. The only thing that I am alergic is Penicillin and Ampicilin. 2) Any other medical problems? No 3) An Emergency contact person. Fernando Babilonia. Telf: 646 752 6557 4) What food are you planning on bringing? If anyone is planning on bringing food that needs to be heated, cooked, or boiled i need to re-calculate how much fuel we need for the stove incase the rain prevents us from lighting a fire. I am planning to take fast easy food like tuna or sandwiches. The only thing that i am planning to use heat is to boil water for instant tea and also I planning to have some hotdogs at dinner. -Rodney ___ 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
[gmx-users] pull code absolute reference artifacts
Hello, I have a question about the following grompp 4.0.4 warning: "You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts." While I do realize that this is an excellent error message containing lots of information, I am still unclear about how to proceed. Why does my system not have an absolute reference? Is it because I have pbc and center of mass motion removal? Exactly what types of artifacts are expected? Is there a simple solution? I am trying to hold my peptide in the center of a water box. I realize that there is no "center" and everything in pbc, but I need to do it nevertheless. Here are my .mdp options: pull= umbrella pull_geometry = distance pull_dim= Y Y Y pull_ngroups= 1 ;pull_group0 = pull_group1 = peptide_A pull_k1 = 500 pull_init1 = 0.00 nsteps = 25 ; REMOVE_FOR_EM tinit = 49000 ; REMOVE_FOR_EM dt = 0.004 ; REMOVE_FOR_EM nstxout = 25 ; REMOVE_FOR_EM nstvout = 25 ; REMOVE_FOR_EM nstfout = 25 ; REMOVE_FOR_EM nstenergy = 25000 ; REMOVE_FOR_EM nstxtcout = 25000 ; REMOVE_FOR_EM nstlog = 25; REMOVE_FOR_EM gen_vel = no unconstrained-start = yes integrator = sd gen_seed= -1 comm_mode = linear nstcomm = 1 comm_grps = System nstlist = 5 ns_type = grid pbc = xyz coulombtype = PME rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 vdwtype = cut-off rvdw_switch = 0 rvdw= 1.4 rlist = 0.9 DispCorr= EnerPres Pcoupl = Berendsen ; REMOVE_FOR_EM pcoupltype = isotropic ; REMOVE_FOR_EM compressibility = 4.5e-5 ; REMOVE_FOR_EM ref_p = 1. ; REMOVE_FOR_EM tau_p = 4.0; REMOVE_FOR_EM tc_grps = System ; REMOVE_FOR_EM tau_t = 1.0; REMOVE_FOR_EM ld_seed = -1 ; REMOVE_FOR_EM ref_t = 300. ; REMOVE_FOR_EM gen_temp= 300. ; REMOVE_FOR_EM constraints = all-bonds ; REMOVE_FOR_EM constraint_algorithm= lincs ; REMOVE_FOR_EM lincs-iter = 1 ; REMOVE_FOR_EM lincs-order = 6 ; REMOVE_FOR_EM ___ 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
