I am using md-vv as an integrator but if I use m , I don't see this drift
(movement) in my system.
This is also another problem that I could not figure out.
On Mon, Jun 15, 2015 at 6:04 PM, gozde ergin wrote:
> Hi Mark,
>
> What do you mean by saying "thing"? Is phase changing?
>
> I visualized
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, beside
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 computatio
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 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 prote
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.
Ot
It is easier to reproduce hydrogen bond parameters without LJ on hydrogen.
On Mon, Jun 15, 2015 at 12:57 PM, Marcelo Depólo
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 are set 0), while HC
>
If your protein structure is retained, your procedure is all right.
On Mon, Jun 15, 2015 at 5:04 AM, Ming Tang 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 system in NPT. Is
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 U
On Sun, Jun 14, 2015 at 6:54 PM, Jan Jirsák 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 think that simul
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
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
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 wrote:
> Hi all,
>
> My system has 560 water molecules covered by 50 organic molecules. I run
> the simulation for
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 8.464e-
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/l9mJesD,ggDDZtb#0 (first pic)
I just could not understand what is going on after 7.5 ns?
Also I am doing this simulation to calcul
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 lin
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
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 wrote:
> I am trying to use GMXPBSAS to calculate the ligand binding energy, but
> this
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
On Mon, Jun 15, 2015 at 8:50 AM Albert 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 depends on the o
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 eq
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 pressure
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 Op
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