[gmx-users] Conflicting atom names when using g_density

Hi Everyone, I am having an awkward situation. I want to use g_density to get the density profile of a lipid bilayer. At first glance, it looks like a trivial task. But for my case, it's not because I have conflicting atom names from two different molecules. I am using GROMOS 53a6. In DPPC

[gmx-users] Molecule removal by g_membed

Hi All, I am simulating a system of lipopeptides embedded into a lipid bilayer. I have a question about how g_membed works. My bilayer has three kinds of lipids. Let's call them lipid_1, lipid_2, lipid_3. Sodium ions are used to balance the charges. When I invoke g_membed, it will ask for which

[gmx-users] Re: Use pull code to restrain the COM

it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Aw: [gmx-users] Umbrella sampling - position restraints (lloyd riggs) 2. Use pull code to restrain the COM (Bin Liu) 3. Re: Use pull code to restrain the COM (Justin Lemkul) 4. Re: Trying to replicate

[gmx-users] Use pull code to restrain the COM

Hi All, I would like to restrain the COM of a molecule, say a protein, in my simulation. I found the pull code can do the job. However, I am not sure about several parameters in the .mdp file. For example, if I want to restrain the COM of the protein in only z direction, but not rigidly, I can

[gmx-users] Re: gmx-users Digest, Vol 111, Issue 53

10, 2013 at 9:13 AM, Bin Liu fdusuperstr...@gmail.com wrote: Hi All, For the convenience of visualization, I need to remove the jump of one component (say a protein) of the system at the boundary. I don't need to, or say I need not to remove the jump of the other components (say a lipid

[gmx-users] AVX2 SIMD intrinsics speed boost

Hi all, If my understanding is correct, GROMACS parallelization and acceleration page indicates AVX2 SIMD intrinsics can offer a speed boost on a Haswell CPU. I was wondering how much performance gain we can expect from it. In another word, what's the approximate speed increase if we run a

[gmx-users] How to apply trjconv -nojump to a part of a system

Hi All, For the convenience of visualization, I need to remove the jump of one component (say a protein) of the system at the boundary. I don't need to, or say I need not to remove the jump of the other components (say a lipid bilayer), since otherwise the system will look falling apart. I

[gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme

Hi All, In GROMACS 4.6.x series, Verlet cutoff scheme is introduced to enable OpenMP parallelization and GPU acceleration. Then some new run parameters are introduced to control the use of Verlet cutoff scheme. However, I noticed the GROMACS manual doesn't give in-depth knowledge on some

[gmx-users] Re:The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme

Dear Mark, Could you elaborate on your answer? In my group cutoff scheme, I used ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.3 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.3 ;