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 > 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. > > Not sure. Try replacing the cylinder with direction or so.
pull_geometry = direction or distance (together with pull_dim= N N Y) works fine. This is why I wonder why only cylinder gives this unexpected result. I would prefer to use cylinder if it is possible. > Emma > >> Thanks! >> >> Best regards, >> Emma -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> * 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. > [email protected] http://folding.bmc.uu.se-- > gmx-users mailing list [email protected] > 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 [email protected]. > * 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. [email protected] http://folding.bmc.uu.se-- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
