Steered MD pulling in Gromacs ?

This is the error message :

ERROR 1 [file md_pull.mdp]: When the maximum distance from a pull group reference atom to other atoms in the group is larger than 0.5 times half the box size a centrally placed atom should be chosen as pbcatom. Pull group 1 is larger than that and does not have a specific atom selected as reference atom.

Pull group natoms pbc atom distance at start reference at t=0

1 9518 4759

2 2993 11015 4.661 nm 4.661 nm

Estimate for the relative computational load of the PME mesh part: 0.18This run will generate roughly 1924 Mb of datawriting run input file...

I have also attached the mdp file.

I am following Justin Lemkul's Umbrella Sampling tutorial.

i have a nano particle and lipid system and i want to move the nano toward the COM of lipid. how can i perform this in GROMACS? the motion is in the Z-axis

it will be preferable if there is an mdp file or a link

thanks

Dear all,

I am looking for a way to restrain the center of mass (COM) of two different molecules bathed in water, using GROMACS 2018. The only thing close I found on gromacs that does this is the pull module embedded in the mdp files. I want to clarify that I want to restrain each molecules (COM) to a different and specific coordinate in my simulated box. Indeed the pull module has an option - pull-coord1-geometry = direction, where I can set the origin (pull-coord1-origin= 0 0 0, for example) and a vector directing the movement of the COM (pull-coord1-vec= 1 1 1) with time (pull-coord1-rate = 0.01nm/ps). However I don’t want my COM to move in time, I want it stationary in a specific coordinate throughout my entire simulation time. I see that I can set a parameter - pull-coord1-start = no - so that it doesn’t start moving towards my vector and stays in what I labeled “origin”.

With all that said, when running my simulations, it looks like my specification in the mdp file lead to no restraints, and it looks like my molecules defuse freely without an energetic bias towards my specified origin coordinate. Here are my mdp settings:

pull = yes pull-ngroups = 2 pull-group1-name = NAH pull-group2-name = RAT

pull-ncoords = 2

pull-coord1-type = umbrella pull-coord1-geometry = direction pull-coord1-groups = 0 1 pull-coord1-dim = Y Y Y pull-coord1-origin = 3.75 2.5 2.5 pull-coord1-vec = 1.0 1.0 1.0 pull-coord1-k = 10000.0 pull-coord1-rate = 0.0 pull-coord1-init = 0 pull-coord1-start = no

pull-coord2-type = umbrella pull-coord2-geometry = direction pull-coord2-groups = 0 2 pull-coord2-dim = Y Y Y pull-coord2-origin = 3.75 2.5 2.5 pull-coord2-vec = 1.0 1.0 1.0 pull-coord2-k = 10000.0 pull-coord2-rate = 0.0 pull-coord2-init = 0 pull-coord2-start = no

where pull-coord2-init = 0 is supposedly irrelevant to the “direction” type of pulling.

If anybody has any experience with this pulling direction technique and might point me to where my settings are wrong, Id be extremely thankful.

Best to all, Ilan Shumilin

I have used CHARMM-GUI to create a small nanoparticle and added some citrate molecules to the box. i want to apply SMD to the citrate to cap the nanoparticle. i am using the attached mdp for doing SMD, however, it gives a warning when using grompp:

You are using an absolute reference for pulling, but the rest of the

system does not have an absolute reference. This will lead to artifacts.

when i add the -maxwarn 1 argument and continue for the dynamics, it says:

Fatal error:

149 particles communicated to PME rank 4 are more than 2/3 times the cut-off

out of the domain decomposition cell of their charge group in dimension x.

This usually means that your system is not well equilibrated.

However when i comment the pull commands in the mdp file, it works well.

Can someone help me with this?

thanks

During MD simulation, tetrameric protein diffuses in the simulation box and ends up crossing the periodic boundaries. One of four chains is jumping to the other side of the simulation box. For my analysis, I need all chains together and centered. 

I tried to use pbc wrap in VMD. But after wrapping the trajectory file, some of atoms are being transformed in an awkward way so I end up seeing stretches while visualizing the protein in new cartoons mode. I am guessing it's because of center of mass of my selection moving significantly. 

The command I have used:

pbc wrap -center com -centersel "protein" -compound residue -all

I could not find a way to fix that, somebody else reported a similar problem in vmd mailing list, so far no replies.

Any suggestions?

Hi everyone. I am trying to replicate an homology modeling protocol. Right now, I am in the TM refinement part which is made in GROMACS, but I don’t understand how to perform the following “Distance restraints are applied between the backbone O and i +4 backbone N, with r0 =0.28 nm, r1 =0.30 nm and r2 =0.31 nm”. I read that the “gmx genrestr” command is used for distance restraint, but I don’t know how to use it to do the mentioned step.

Here I attach the protocol.

Thank you in advance for your help.

Hello every body

I want to calculate the center of mas for a protein. I want to know which amino acid the center of mass hold on.

pleas give me a full help.

thanks

I need a way to rotate my entire system (DNA and solvent) such that the axis of the DNA lies along the x-axis, but I want the periodic boundaries to be preserved. I added pictures of my system before and after rotation.

How can I edit things in such a way that the entire system is rotated, but molecules stay within the box? (basically the water molecules that were rotated down and went outside the box should reappear up inside the box)

Thank you in advance!