I am using following pull code in the steered md simulation in gromacs for pulling a molecule across the plasma membrane model.
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_ngroups =2
pull-ncoords =1
pull_coord1_groups = 1 2
pull_group1_name = NPROT_ref
pull_group2_name = LIG
pull_coord1_rate = -0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
pull_nstxout = 1000 ; every 2 ps
pull_nstfout = 1000 ; every 2 ps
But molecules is not moving beyond the centre of the membrane model where z=0
I read one online tutorial at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html , provided by Dr. Justin. (may be i misunderstood the tips provide at this web page, can anyone correct me, if i am wrong and also did not understood how to use pull_geometry = position, as there is no such option I found on the mdp option web page of the gromacs)
then I used following code
pull_geometry = direction
pull_vec1 = 0 0 1
I got the following error
Fatal error:
Distance between pull groups 1 and 2 (5.763902 nm) is larger than 0.49 times the box size (4.446700).
where as box size is 10. 327 10.327 8.89
some where I am making mistake in the pull code setting, but not able to find out. can anyone suggest me where I am doing wrong, and what could be the possible pull code parameters.
From what I can understand, you are trying to pull a molecule INTO a bilayer and it stopped at the midpoint of the bilayer? Did you group your molecules correctly? The last fatal error means that the distance between the two pull groups are larger than half the box size. This is a limitation if you set "pull_geometry = direction". "pull_geometry = position" seems to have been taken out of GROMACS 5.0, it is still around in GROMACS 4.6.5 which is what I use.
Also, you have used "pull_geometry = distance". If I'm not wrong, once the distance between the two groups is zero, it will not move anymore.
One last comment, have you visualized your run and see where exactly your molecule is moving?
thanks for the reply
it's moving up to the centre of the bilayer from the bulk water when i visualized the trajectory and the explanation you gave seems correct. but, what could be the possible solution for pull_geometry = position. if i want to use gromacs 5.0.4
with regards
mahender singh
Are you performing pulling using the direction option after you've completed pulling (the molecule stops at z=0) using the distance option?
If this is the case, then I guess that there are periodic image interactions in the case of your first simulation. The distance between your groups at the end of the first simulation is large enough that they interact with their periodic images in the adjacent box. I guess that this is what the second error points to. You can check for the same using the g_mindist utility of gromacs along with the -pi flag. If there are periodic image interactions, then you will need a larger simulation box to pull the groups for the distance you want to.
I'm not terribly sure how to get "pull_geometry = position" in Gromacs 5.x. I think what I would do is to increase the box size and use "pull_geometry = direction", with probably a little arithmetic to make sure that half the box size is larger than half of the maximum distance you want to pull. Have you also tried asking in the Gromacs mailing list?
Dear Mahender,
Can I ask you how you have used gmx distance syntax? i am having problem finding distance between my two proteins. one of my proteins is a peptide that I have pulled in x direction. thank you
Dear Ayesha
You can find the syntax detail in the following link
http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
hope it will solve the problem of gmx distance syntax
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