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Wall parameters and pbc
- batsaikhan_b
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5 years 9 months ago #7706
by batsaikhan_b
Wall parameters and pbc was created by batsaikhan_b
Dear Experts,
I an new user. I would like to use pbc only in the xy axises and two walls along the z axis in gromacs.
I checked the gromacs manual and looked for through the internet. I could not find well document for the CG MD simulation with wall settings.
I also tried a number of times with the following options
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xy
verlet-buffer-tolerance = 0.005
nwall = 2 ; wall at z=0 and z=z-box
wall-type = 10-4 ;
wall-atomtype = C5 C5
wall-density = 120 120
wall-r-linpot = -2 -2
ewald-geometry = 3dc ; Only Ewald sum compatible with slab geometry,$
wall-ewald-zfac = 3
comm-mode = none
refcoord_scaling = all
I still receive sorting error or core dumping.
Please advice me.
I an new user. I would like to use pbc only in the xy axises and two walls along the z axis in gromacs.
I checked the gromacs manual and looked for through the internet. I could not find well document for the CG MD simulation with wall settings.
I also tried a number of times with the following options
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xy
verlet-buffer-tolerance = 0.005
nwall = 2 ; wall at z=0 and z=z-box
wall-type = 10-4 ;
wall-atomtype = C5 C5
wall-density = 120 120
wall-r-linpot = -2 -2
ewald-geometry = 3dc ; Only Ewald sum compatible with slab geometry,$
wall-ewald-zfac = 3
comm-mode = none
refcoord_scaling = all
I still receive sorting error or core dumping.
Please advice me.
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- riccardo
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5 years 9 months ago #7707
by riccardo
Replied by riccardo on topic Wall parameters and pbc
Hi,
First of all, if you found some documentation/example of AA MD with walls, did you try it and, if so, did it work?
I remember playing around with walls some time ago and getting some weird behaviors. I was, however, trying a system with only one wall and 2D pbc.
I can't really tell you what is going wrong with your parameters, but perhaps you can consider trying a 3D periodic system where you include some vacuum between the walls. In this way, you will still be formally running a 3D periodic system (pbc = xyz), but you will effectively have a 2D system.
First of all, if you found some documentation/example of AA MD with walls, did you try it and, if so, did it work?
I remember playing around with walls some time ago and getting some weird behaviors. I was, however, trying a system with only one wall and 2D pbc.
I can't really tell you what is going wrong with your parameters, but perhaps you can consider trying a 3D periodic system where you include some vacuum between the walls. In this way, you will still be formally running a 3D periodic system (pbc = xyz), but you will effectively have a 2D system.
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- batsaikhan_b
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5 years 9 months ago #7710
by batsaikhan_b
Replied by batsaikhan_b on topic Wall parameters and pbc
Thank you for your reply. I could not have any tutorial, however, I found some research works that used the 2D pbc and with two walls. There is no specific information about the whole settings.
I do not know which atom type is good for the wall-atomtype in the Martini force field. If you have any suggestion, please advice me. I tried many times with wall-atomtype = C1 C1 to C5 C5 even D.
3D pbc is still okay. I performed the test run of simulation. How can I use only one wall system, please advice me?
I am really a new user of these type of simulations.
Best regards,
Batsaikhan
I do not know which atom type is good for the wall-atomtype in the Martini force field. If you have any suggestion, please advice me. I tried many times with wall-atomtype = C1 C1 to C5 C5 even D.
3D pbc is still okay. I performed the test run of simulation. How can I use only one wall system, please advice me?
I am really a new user of these type of simulations.
Best regards,
Batsaikhan
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- riccardo
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5 years 9 months ago #7713
by riccardo
Replied by riccardo on topic Wall parameters and pbc
Are you saying that a two walls system with 3D pbc works?
Do you need one or two walls?
Before looking at which parameters (including bead types) work best for the walls in a Martini scenario, I would make sure that you can run a simulation with walls using standard settings (i.e., at atomistic resolution). I would thus try to find some work in the literature where such simulations are run (and where settings are also mentioned). Alternatively, you could try to run some test simulations with issuing GROMACS default settings for walls. Have you tried that?
Do you need one or two walls?
Before looking at which parameters (including bead types) work best for the walls in a Martini scenario, I would make sure that you can run a simulation with walls using standard settings (i.e., at atomistic resolution). I would thus try to find some work in the literature where such simulations are run (and where settings are also mentioned). Alternatively, you could try to run some test simulations with issuing GROMACS default settings for walls. Have you tried that?
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