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?
Thanks!
Best regards,
Emma --
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