Re: [gmx-users] Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)
On 2012-10-08 09:05, Emma Eriksson wrote: Thank you David for your response. Please see my reply below. On 2012-10-04 11:50, Emma Eriksson wrote: Dear all, I am using the pull code in Gromacs 4.5.5 to constrain the distance in one direction (z) between a small molecule and a lipid bilayer. I run separate simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder. The pull parameters are the following: pull = constraint pull_geometry = cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DMPC pull_group1 = 2 pull_vec1 = 0 0 1 pull_init1 = x I have previously been using the same methodology in 4.0.5 without problems. When i run grompp in 4.5.5 I get the following error: Fatal error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310) The source of the first value, which should be the distance of pull group 1 is for me unknown. A value of ~4 is generated for all systems no matter what z distance is actually betwen the two groups (0-4 nm), so the value has no connection to the z distance between the groups. The second value is 0.5 times the x box length. I have read through pull.c, but I cannot find an explanation to why the x direction seems to be considered and not the z direction. When I run grompp with pull_geometry = distance or direction together with pull_dim = N N Y there is no problem. As I am not sure of the source of this error when running with cylinder I do not know if it is only related to the check or if the following simulation would be affected if I uncomment the check. Any suggestions to why this is happening and what I can do about it? Check the other pull_XXX values in mdout.mdp You have not specified all of them above, e.g. pull_direction? The pull parameter section in mdout.mdp are the following: ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = constraint ; Pull geometry: distance, direction, cylinder or position pull_geometry= cylinder ; Select components for the pull vector. default: Y Y Y pull_dim = Y Y Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1.0 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = no pull_nstxout = 10 pull_nstfout = 1 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = DMPC pull_weights0= pull_pbcatom0= 0 pull_group1 = 2 pull_weights1= pull_pbcatom1= 0 pull_vec1= 0 0 1 pull_init1 = 0 pull_rate1 = 0 pull_k1 = 0 pull_kB1 = 0 I did not specify pull_dim as I understood it from the manual that this should not be used this for pull_geometry = cylinder (however, pull_dim will be set to the default Y Y Y in mdout.mdp). I specify pull_vec1 = 0 0 1, which should give the pull direction (z in this case). Did I misunderstand this somehow? When I specify pull_dim = N N Y I do not get any error with grompp, but instead I obtain the following: Pull group natoms pbc atom distance at start reference at t=0 0 5888 2944 149 20922 3.685 0 The distance between the two groups should be 0 but the program interpret is as 3.685, which is a value that I do not know where it comes from. I do not know what other options I can try or what is wrong here. Do you have any suggestion what is going on? Thank you. Not sure. Try replacing the cylinder with direction or so. Emma Thanks! Best regards, Emma -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se-- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol.,
[gmx-users] Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)
Thank you David for your response. Please see my reply below. On 2012-10-04 11:50, Emma Eriksson wrote: Dear all, I am using the pull code in Gromacs 4.5.5 to constrain the distance in one direction (z) between a small molecule and a lipid bilayer. I run separate simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder. The pull parameters are the following: pull = constraint pull_geometry = cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DMPC pull_group1 = 2 pull_vec1 = 0 0 1 pull_init1 = x I have previously been using the same methodology in 4.0.5 without problems. When i run grompp in 4.5.5 I get the following error: Fatal error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310) The source of the first value, which should be the distance of pull group 1 is for me unknown. A value of ~4 is generated for all systems no matter what z distance is actually betwen the two groups (0-4 nm), so the value has no connection to the z distance between the groups. The second value is 0.5 times the x box length. I have read through pull.c, but I cannot find an explanation to why the x direction seems to be considered and not the z direction. When I run grompp with pull_geometry = distance or direction together with pull_dim = N N Y there is no problem. As I am not sure of the source of this error when running with cylinder I do not know if it is only related to the check or if the following simulation would be affected if I uncomment the check. Any suggestions to why this is happening and what I can do about it? Check the other pull_XXX values in mdout.mdp You have not specified all of them above, e.g. pull_direction? The pull parameter section in mdout.mdp are the following: ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = constraint ; Pull geometry: distance, direction, cylinder or position pull_geometry= cylinder ; Select components for the pull vector. default: Y Y Y pull_dim = Y Y Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1.0 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = no pull_nstxout = 10 pull_nstfout = 1 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = DMPC pull_weights0= pull_pbcatom0= 0 pull_group1 = 2 pull_weights1= pull_pbcatom1= 0 pull_vec1= 0 0 1 pull_init1 = 0 pull_rate1 = 0 pull_k1 = 0 pull_kB1 = 0 I did not specify pull_dim as I understood it from the manual that this should not be used this for pull_geometry = cylinder (however, pull_dim will be set to the default Y Y Y in mdout.mdp). I specify pull_vec1 = 0 0 1, which should give the pull direction (z in this case). Did I misunderstand this somehow? When I specify pull_dim = N N Y I do not get any error with grompp, but instead I obtain the following: Pull group natoms pbc atom distance at start reference at t=0 0 5888 2944 149 20922 3.685 0 The distance between the two groups should be 0 but the program interpret is as 3.685, which is a value that I do not know where it comes from. I do not know what other options I can try or what is wrong here. Do you have any suggestion what is going on? Thank you. Emma Thanks! Best regards, Emma -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se-- 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
