[gmx-users] Re: 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
Mon Oct 8 09:05:02 CEST 2012

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:
; 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.


> Thanks!
> 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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