[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)

[David van der Spoel]

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.

> Emma
>
>> 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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-- 
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