Re: [gmx-users] how can we merge SOL into protein.itp?

On Mon, Jun 15, 2015 at 8:50 AM Albert mailmd2...@gmail.com wrote: Hello: I've got two highly conserved crystal water molecules in my simulation system, and I would like to treat them as a part of protein. What are you trying to achieve? Whether you need to do something like you tried below

Re: [gmx-users] how can we merge SOL into protein.itp?

I am trying to use GMXPBSAS to calculate the ligand binding energy, but this program will delete all solvent molecules automatically. In this case, I have to merge the protein and crystal water into a single .itp file so that GMXPBSA treat the crystal water as a part of protein However, I

Re: [gmx-users] how can we merge SOL into protein.itp?

Hi, In that case, gmx pdb2gmx -merge and/or -chainsep probably can be made to work. Maybe you will need to hack your .pdb file to add chain identifiers, not sure. Mark On Mon, Jun 15, 2015 at 2:52 PM Albert mailmd2...@gmail.com wrote: I am trying to use GMXPBSAS to calculate the ligand

Re: [gmx-users] Performance of NVIDIA GTX980 in PCI-e 3.0 x8 or x16 slots ?

On 11.06.2015 14:07, David McGiven wrote: Your 1-3% claim is based on the webpage you linked ? Is it reliable to compare GPU performances for gromacs with those of 3D videogames ? OK, you got me on this. As much as I'd wish I cannot really back up my claim of comparability. I have been out of

Re: [gmx-users] Potential Energy-Umbrella sampling

Hi, Your trajectory went from one thing to a completely different thing, so what did your visual inspection of the trajectory tell you? Mark On Mon, 15 Jun 2015 17:54 gozde ergin gozdeeer...@gmail.com wrote: Hi all, My system has 560 water molecules covered by 50 organic molecules. I run

[gmx-users] Potential Energy-Umbrella sampling

Hi all, My system has 560 water molecules covered by 50 organic molecules. I run the simulation for 20 ns and here is my potential energy figure. http://imgur.com/DrBvnjs I just could not understand what is going on after 7.5 ns? Also I am doing this simulation to calculate the PMF. On the

[gmx-users] Explicit Hydrogen LJ param

Hi all! It might be a silly question, but I am wondering why explicit hydrogens do not have LJ parameters in Gromos forcefields (they are set 0), while HC hydrogens (aromatic) has some value: ;name at.num masscharge ptype c6 c12 HC1 0.000 0.000 A

Re: [gmx-users] Potential Energy-Umbrella sampling

Hi Mark, What do you mean by saying thing? Is phase changing? I visualized in VMD but could not manage to really captured the difference before 7.5 ns and after 7.5 ns. Also because during the simulation all bulk is moving in the box but distances between pullgroups stays constant so it is not

[gmx-users] GMX 5.0.5 x2top segfaults

Ahoy all. What's going on with the latest version of x2top? It spectacularly segfaults at the point of doing dihedrals. Identical setup (local oplsaa.ff with some customization) works flawlessly with 4.6.5 and the resulting topologies are all perfectly reasonable. Not cool. Any suggestions,

Re: [gmx-users] Fatal error: Atom type AU (residue LIG) not found in atomtype database

Hello, We are trying to simulate gold nanoparticles (which we called the residue LIG) and we are trying to add the gold parameters in GROMACS using opls or charmm. The parameters are obtained from the article Effect of Gold Nanoparticle on Structure and Fluid

Re: [gmx-users] Vacuum simulation in Gromacs 5

On Sun, Jun 14, 2015 at 6:54 PM, Jan Jirsák janjir...@gmail.com wrote: Hi, I did the test and found out that -nt 8 is even slower than -nt 1 !! FYI: -nt is mostly backward compatibility option and for clarity it's best to use either -ntmpi or -ntomp, depending on what you mean. However, I

Re: [gmx-users] Explicit Hydrogen LJ param

It is easier to reproduce hydrogen bond parameters without LJ on hydrogen. On Mon, Jun 15, 2015 at 12:57 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Hi all! It might be a silly question, but I am wondering why explicit hydrogens do not have LJ parameters in Gromos forcefields (they

[gmx-users] Problem with GROMACS and AMBER ff

Hi all. We doing a MD simulation with GROMACS using AMBER force field. During the simulation the disulfide bonds are increasing over time. We set the bridge manually with pdb2gmx. Someone help us? -- ´´Las oportunidades son como los amaneceres, si te demoras un poco las pierdes´´. -- Gromacs

Re: [gmx-users] confusion on NPT MD simulation

If your protein structure is retained, your procedure is all right. On Mon, Jun 15, 2015 at 5:04 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Justin, I got a problem making me confused for weeks. I found 2 journals, in which the author kept parts of their protein to equilibrate their

Re: [gmx-users] confusion on NPT MD simulation

Dear Justin, I got a problem making me confused for weeks. I found 2 journals, in which the author kept parts of their protein to equilibrate their system in NPT. Is there any other methods to keep atoms fixed during NPT equilibrium besides freezing them? As you mentioned, freezing and

[gmx-users] Deformation of bio-polymer

Dear All users and developersI want to study the pressure effects on the mechanical properties of a bio-polymer (that is, Young modulus or stress-strain curve) by uni-axial deformation of simulation box in z-direction via all-atom MD simulation. For this purpose, the simulation cell was first

[gmx-users] how can we merge SOL into protein.itp?

Hello: I've got two highly conserved crystal water molecules in my simulation system, and I would like to treat them as a part of protein. So I am must wondering how can we merge it into protein.itp? I put them into protein.pdb and run command: pdb2gmx -f protein.pdb -o gmx.gro and I found

[gmx-users] Crash of DD with periodic_molecules

Dear All, We are stuck with an error in domain decomposition for graphene layer, which is periodic in XY plain (periodic_molecules=yes). The system runs perfectly on one node, but when we try to use more than 1 MPI process it crashes regardless of what we do: Using 2 MPI processes Using 4

Re: [gmx-users] Deformation of bio-polymer

What is the problem to set EACH pressure components using anisotropic pressure coupling, see MDP file? Remember that barostats do not like non-equilibrium MD. If the condensed matter system has already been equilibrated under the desired conditions, I would just do pulling in the NVT ensemble.

Re: [gmx-users] how can we merge SOL into protein.itp?

I believe you need to attach waters to the protein harmonically and T-couple them separately during MD. On Mon, Jun 15, 2015 at 3:49 AM, Albert mailmd2...@gmail.com wrote: Hello: I've got two highly conserved crystal water molecules in my simulation system, and I would like to treat them

Re: [gmx-users] Performance of NVIDIA GTX980 in PCI-e 3.0 x8 or x16 slots ?

Good data Mirco, but let me emphasize that your measurements only reflect the case of heavily GPU-bound workloads! 5-6% performance improvement with PCI-E 3.0 vs 2.0 is about the maximum you'll see when, like in RF runs where, we there is no enough CPU work to fully overlap with the GPU