I have gone through the pull parameters in version 4.0 and 4.5 a bit more after our previous discussion and I have found the following related to the value of pull_init1. pull_geometry = distance or direction generate the same distance at start with grompp no matter what value is set to pull_init1, and it is the same in version 4.0 as in 4.5. However, for pull_geometry = cylinder in version 4.5 I find that the measured distance at start varies with the value on pull_init1. For a molecule at distance -0.026 nm from the reference group (value from version 4.0) I obtain the following with grompp in version 4.5:
pull_init1 = 0 gives start distance -0.026 pull_init1 = 1 gives start distance -0.026 pull_init1 = 2 gives start distance 0.605 pull_init1 = 3 gives start distance 2.596 pull_init1 = 4 gives the error that the distance of the pull group is larger than 0.49 times the box size. In version 4.0, all values of pull_init1 generate the distance at start = -0.026. I will set pull_init1 to -0.026 or use pull_start = yes in this case and it would give the result that I want. From these findings I assumed that the value of pull_init1 was somehow added to the measured distance in version 4.5. However, for another system in which the distance between the groups is -2.996 nm, the following is obtained: pull_init1 = 0 gives start distance -0.465 pull_init1 = 1 gives start distance 1.014 pull_init1 = 2 gives the error that the distance of the pull group is larger than 0.49 times the box size. pull_init1 = 3 gives the error that the distance of the pull group is larger than 0.49 times the box size. pull_init1 = 4 gives the error that the distance of the pull group is larger than 0.49 times the box size. Here, pull_init1 = 3 can thus not be used; opposite to the previous case in which a value of pull_init1 close to the measured distance seemed to work. If I instead use pull_geometry = distance or direction all values of pull_init1 generate the error that the distance of the pull group is larger than 0.49 times the box size. In version 4.0, the value of pull_init1 does, again, not affect the distance at start. I interpret pull_init1 as the reference distance at start (i.e. the initial distance that I want to constrain as I am not pulling the molecule) and I thought that this should not affect the measured distance at start that grompp displays, at least that is what can be concluded from version 4.0. Could someone please help me to figure this out? Thanks. Emma > 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 gmx-users at 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-request at 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. > spoel at xray.bmc.uu.se http://folding.bmc.uu.se-- > gmx-users mailing list gmx-users at 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-request at 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. spoel at 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. 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