[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)

Emma Eriksson emma.eriksson at chem.gu.se
Thu Oct 4 11:50:43 CEST 2012

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?

Best regards,

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