Dear all;
I just found that the water which vmd generates (via add solvation box tool) is three times more dense than regular water at 300k and 1atm! I mean the number of atoms is three times more than what it should be. Do you have any idea how can I fix this issue? what are other softwares that I can use to generate water for lammps simulation?
Regards,
Rostam
Dear all;
I just found that the water which vmd generates (via add solvation box tool) is three times more dense than regular water at 300k and 1atm! I mean the number of atoms is three times more than what it should be.
I seriously doubt that statement. How can this have gone unnoticed for so many years? That you mention a factor of 3 is particularly suspect.
Do you have any idea how can I fix this issue? what are other softwares that I can use to generate water for lammps simulation?
They will probably also be off by a factor of three. 
Axel
you’re right! I’m such a dumb.I think I should sleep now!!
Dear all;
I just found that the water which vmd generates (via add solvation box tool) is three times more dense than regular water at 300k and 1atm! I mean the number of atoms is three times more than what it should be.
I seriously doubt that statement. How can this have gone unnoticed for so many years? That you mention a factor of 3 is particularly suspect.
Do you have any idea how can I fix this issue? what are other softwares that I can use to generate water for lammps simulation?
They will probably also be off by a factor of three.
Axel
But what if I want to generate water in other densities. for example vapour. Is vmd capable of that?
you’re right! I’m such a dumb.I think I should sleep now!!
Dear all;
I just found that the water which vmd generates (via add solvation box tool) is three times more dense than regular water at 300k and 1atm! I mean the number of atoms is three times more than what it should be.
I seriously doubt that statement. How can this have gone unnoticed for so many years? That you mention a factor of 3 is particularly suspect.
Do you have any idea how can I fix this issue? what are other softwares that I can use to generate water for lammps simulation?
They will probably also be off by a factor of three.
Axel
But what if I want to generate water in other densities. for example vapour. Is vmd capable of that?
No need. Adjust the volume of your box as needed with change_box and turn on the heat.
I think you are changing the problem!
Another question, If I have two different materials in a same box can I use npt for all atoms? I’ve done it and I got strange temperature profile.
Thanks for the answers dear Axel.
But what if I want to generate water in other densities. for example vapour. Is vmd capable of that?
No need. Adjust the volume of your box as needed with change_box and turn on the heat.
I think you are changing the problem!
Another question, If I have two different materials in a same box can I use npt for all atoms? I’ve done it and I got strange temperature profile.
Sure you can. Why not? The fix doesn’t care. You can have 10 materials if you want.
Better you check how you compute the temperature profile and how you have equilibrated the system.
I don’t think so. Because I’ve done a simulation which I have two phases.A solid and a liquid.
I first equilibrated the system with npt for all and I got a strange result in temperature profile ( which was done with compute temp/profile). The same thing happen when I use nvt for all. One of my friend in georgia tech also got the same results for a solid-liquid interface.I saw a thesis which used berendsen thermostat for all atoms and I can’t understand why this happens.
I think you are changing the problem!
Another question, If I have two different materials in a same box can I use npt for all atoms? I’ve done it and I got strange temperature profile.
Sure you can. Why not? The fix doesn’t care. You can have 10 materials if you want.
Better you check how you compute the temperature profile and how you have equilibrated the system.
I don’t think so. Because I’ve done a simulation which I have two phases.A solid and a liquid.
I first equilibrated the system with npt for all and I got a strange result in temperature profile ( which was done with compute temp/profile). The same thing happen when I use nvt for all. One of my friend in georgia tech also got the same results for a solid-liquid interface.I saw a thesis which used berendsen thermostat for all atoms and I can’t understand why this happens.
There is far too little information to make a statement on that, but don’t you think it is possible, you both made the same mistake? The thermostat should not affect this significantly or else the system was not properly equilibrated. With a two phase system this can easily happen, if you are not careful.
Again, think about probabilities: lammps has been around for a long time and people have done a lot of multi-phase simulations. Do you think it is likely that all of them overlooked such a big problem?
With regards to this question, you can build various kinds of
waterboxes and mixtures of water with other objects using moltemplate.
It can build both LAMMPS data files, and input scripts containing
force-field information.
nanotube+water
http://moltemplate.org/images/nanotube+water/nanotube+walls+water_side_pbc_t=0ps.jpg
waterSPCE+Na+Cl
http://moltemplate.org/images/waterSPCE+Na+Cl/waterSPCE+Na+Cl_t=0.jpg
http://moltemplate.org/images/waterSPCE+Na+Cl/waterSPCE+Na+Cl_t=100ps.jpg
(SPC/E and TIP3P water molecule types, parameters, charges, etc are
already included. If you create a new type of solvent, please email
it to me and I will post it.)
There's also an "ice_crystal" example in the online examples which you
can download at moltemplate.org. (You can even combine ice with
liquid water at NPT in the same simulation, and use fix rigid if you
want to keep the ice from melting. See a discussion of this at
http://lammps.sandia.gov/threads/msg41778.html)
Packing water around irregularly shaped objects is more difficult, but
possible in moltemplate. For example:
http://lammps.sandia.gov/threads/msg34435.html
Alternately, you can define the system using moltemplate, and pack
water molecules around the solute using packmol. Here's an example
using packmol to pack lipids around a protein:
http://moltemplate.org/examples/vesicle_Brannigan2005+Bellesia2010.html
You can do all this with topotools too.
Cheers!
Andrew
what are other softwares that I can use to
generate water for lammps simulation?With regards to this question, you can build various kinds of
waterboxes and mixtures of water with other objects using moltemplate.
It can build both LAMMPS data files, and input scripts containing
force-field information.
sorry, that post was a bit self-centered.
Check out:
http://lammps.sandia.gov/prepost.html
There's also this program
http://sourceforge.net/projects/moleculardynami/
Cheers
Andrew