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 1 49 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 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 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.se http://folding.bmc.uu.se-- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists