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HI Berk, Thanks for your reply! Questions related the implicit Walls. a) When I use PBC =xyz in combination with nwall=2, I get the following error ERROR: walls only work with pbc=xy But If I use pbc=xy, there is no periodic image in the Z direction, why should we use "wall_ewald_zfac"=2~3? c) Even though I have used half of the processors for -npme, there is still more than 20% is lost due to PME have more work to do. Is there any idea to improve the performance? The following is the parameters for the walls I try to simulate the graphine substrate. ; WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall = 2 wall_type = 9-3 wall_r_linpot = 0 wall_atomtype = opls_135 opls_135 wall_density = 114 114 wall_ewald_zfac = 3 Berk Hess wrote: Hi, Nearly all the information is in the mdp options page, but it is a bit concise. The only really missing information is that there is not cut-off for the wall. All atoms feel the force of one or both walls.The density is required to determine the interaction strength of the wall for the 9-3 and 10-4 options. The LJ potential is integrated over the volume behind the wall or the plain of the wall, which requires a LJ particle density. Berk Date: Mon, 21 Sep 2009 10:02:29 +0200 From: qia...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] question about the implicit walls Hi, Is anyone who can clear the "Walls" feature in the gmx 4.0.x? Same as Yves (see the end), I cannot find any related reference or publication citing it. Generally the potential on wall is in continuum format. But if it is also true here, what the "wall_density" for? I guess it is based on a lattice model. If I want to build silicon or graphene walls, what kind of values is suitable for them? Any reference? regards, Baofu Qiao [gmx-users] Implicit walls. Yves Dubief Thu, 11 Jun 2009 03:32:11 -0700 Hi, I am using the implicit wall method available in 4.0.x and I cannot seem to find any published work on the method, aside from the manual. I think I have an overall understanding of the method, but I am not confident about some key details: - Is the force generated from the wall derived from a continuum representation of the wall based on the surface density, or from a lattice of virtual atoms? I am leaning toward #1 just because it works great under NPT - What is the depth of the virtual wall when wall_r_linpot=0? Is it LJ cutoff? or "zero"? - Are any of developer willing to validate the paragraph we plan on writing in my student thesis and future publications (when it's all ready)? Thank you in advance. Yves _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ |
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