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.
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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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
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