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In the simulation that I have posted , as you can see that my ligand molecule is pulled down . What should I do such that the molecule goes upwards through the protein channel. What changes should I make in the pull.mdp file .
It is a bit impossible to help if you post photos and not the .mdp options you are using to pull the molecule. In general, try to invert the sign of the speed in the .mdp file, this should invert the direction of the pulling
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = Chain_A
pull_group2_name = Chain_B
pull-group2-pbcatom = 4684
pull-pbc-ref-prev-step-com = yes
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = -0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
this is the pull code that i have tried just now . I have put one simulation using this . I used the negative pull rate , is that the same thing that you were talking about
Your set up is pull_coord1_geometry = distance which from the manual is defined as
Pull along the vector connecting the two groups. Components can be selected with pull-coord1-dim.
and your set up is then pull_coord1_dim = N N Y which means that you are pulling along the z coordinate. I do not know what was the set up of the .mdp file, but changing the sign of the rate/speed is for sure the first thing to try. This won’t ensure that the molecule will go thorough the channel, though.
As I said before that I had kept a simulation in which I had assigned a negative sign for the pull rate . The simulation was complete , but what has occured is the ligand didn’t move at all . Should I increase the force .
should i also try to interchange the pull groups as in the simulations that i have performed so far , i have kept my ligand as the group 1 and the protein as group2
I tried simulating the system several times using the negative pull rate , but every time the ligand just didnt move or the simulation stopped stating a fatal error
Fatal error:
Pull reference distance for coordinate 1 (-0.000004) needs to be non-negative
i even tried interchanging the groups , i.e making protein as group 1 and ligand as group 2 , but no positive result .
Making the protein group 1 is usually a good idea, or you could set pull_coord1_groups = 2 1. The first group of the pull coordinate is used as reference to pull the other group. You usually want a large group as reference. But you said that you already tried that.
How long does it take for the simulations to crash? Check the pullx.xvg output file to see where the reference coordinate is (along the pulling dimension). If the reference coordinate (the distance you try to keep the groups at at that step) approaches 0 without the pulled group moving much then you probably need to increase the force constant. If the reference coordinate gets <0 you will get the crash you encountered.
Sir one thing that I noticed in these simulations is that , when the pull rate was non negative value of 0.01 , then the pull happened pretty well in the downward direction which is not desired . This happened well within 100 ps . But when I made the pull rate negative . Even after 110 ps the ligand didn’t seem to move much. In the next trial i tried to increase the pull force from 1000 to 1500 . Then too I got the same result. What might be the reason behind this , should I increase the force even more ?
Sir I’ll also check the .xvg file to see where the system crashes exactly
It will be trying to move the ligand in a (if it’s the second group in pull_coord1_groups) towards the center of the protein, along the Z axis. If there is anything in its way (such as protein atoms) you will need a high (or very high) force constant (and after a while the simulation will probably crash due to the high forces or due to the reference distance becoming negative).
Sir I have just tried this , I have kept the force constant high . And sir you are right, actually in the upward direction where I want the ligand molecule to go , it is encountering too many atoms . Let’s see , i have kept the Job to run . Will update the results
Sir I think , the PDB of the protein channel that I have used is in closed state. Thats the reason why the molecule is not able to move upwards . I need to rebuild the structure by taking the protein channel in its open state .