nemd simulation of tip4p water with non-periodic surface

Dear all,
I’m trying to do NEMD shock simulation of tip4p water. For that purpose I need one direction must be non-periodic to be used along with wall/piston or wall/reflect. But due to the straddling of water molecules across the surface, i’m getting the error “TIP4P hydrogen is missing”. So in this regard can somebody give some suggestion/tricks how to overcome such problem ?

Vishnu

Dear all,
I’m trying to do NEMD shock simulation of tip4p water. For that purpose I need one direction must be non-periodic to be used along with wall/piston or wall/reflect. But due to the straddling of water molecules across the surface, i’m getting the error “TIP4P hydrogen is missing”. So in this regard can somebody give some suggestion/tricks how to overcome such problem ?

I don’t understand your reasoning. It should not matter, if your initial configuration and your input file are correct. This error is quite typically pointing out incorrect setups and settings.

Dear Axel sir,
Initially I took a small water data (494949 Angstrom3) with periodic boundary in all orthogonal direction after a NPT of 1ns, I just replicated it by 12 1 1 in x, y and z direction respectively with b/c of p p p. Then I have done another NPT of 500 ps with p p p and have checked the rdf and all time averaged thermodynamics data to be sure about the equilibration. After getting the water data file I was trying to do NVE with fs p p boundary. So can you please tell me that what settings I need to check, I’m really confused. For the sake of simplicity of the input deck, I have omitted the wall related arrangement and here is my input for your kind perusal. Your hints would be a great help for me, thanks for your time.

Dear Axel sir,
Initially I took a small water data (494949 Angstrom3) with periodic boundary in all orthogonal direction after a NPT of 1ns, I just replicated it by 12 1 1 in x, y and z direction respectively with b/c of p p p. Then I have done another NPT of 500 ps with p p p and have checked the rdf and all time averaged thermodynamics data to be sure about the equilibration. After getting the water data file I was trying to do NVE with fs p p boundary.

Here is your mistake. Simply changing boundaries will not guarantee the integrity of the molecules. That is how you get your error. You either have to post process the restart of the equilibration, for example with a tool like the topotools and pbctools plugins in vmd or a custom program that wraps whole molecules back into the box. Or you first need to generate a gap in your water block with two instances of fix oneway right where the box boundary will be changed from periodic to non-periodic.

So can you please tell me that what settings I need to check, I’m really confused. For the sake of simplicity of the input deck, I have omitted the wall related arrangement and here is my input for your kind perusal. Your hints would be a great help for me, thanks for your time.