[gmx-users] 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)
David van der Spoel
spoel at xray.bmc.uu.se
Fri Oct 5 17:27:35 CEST 2012
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?
> Best regards,
> Emma --
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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
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