Dear All,
I am simulating a tetramer (Alcohol Dehydrogenase with bound NADPH) in
simple spc water in a dodecahedron box. I could easily walk through till the
NVT equilibration step after which every thing seems so right(after 5
steps with time step of 2fs using V-rescale thermostat the system
On 2011-04-03 02.15, Elisabeth wrote:
Dear David,
I followed your instructions and calculated Heat of vaporization of my
alkane once with one molecule in gas phase (no cutoff) and once with
equivalent number of molecules as in liquid phase as Justin suggested.
Results are as follows:
*one
Kishore wrote:
Dear All,
I am simulating a tetramer (Alcohol Dehydrogenase with bound NADPH) in
simple spc water in a dodecahedron box. I could easily walk through till
the NVT equilibration step after which every thing seems so right(after
5 steps with time step of 2fs using V-rescale
Dear All
I have a file which contains afew residues (noncontinuous),
When I use mdrun on a computer(4 cpu) I am facing with the following Error:
Fatal error:
There is no domain decomposition for 4 nodes that is compatible with the
given box and a minimum cell size of 3.28697 nm
Change the number
On 4/04/2011 1:51 AM, mohsen ramezanpour wrote:
Dear All
I have a file which contains afew residues (noncontinuous),
When I use mdrun on a computer(4 cpu) I am facing with the following
Error:
Fatal error:
There is no domain decomposition for 4 nodes that is compatible with
the given box
Dear gmx users,
I’m a NAMD user and want to use gromacs 4.5.4 analysis tools for my NAMD output
files. I have some NAMD output files : output.coor , output.vel , output.dcd
(binary coordinate trajectory output file). Can I convert these output files
into gromacs output files and use gromacs
Hi,
depends on the tool. If the tool just need the coordinates or just
velocities (dcd/vel) you don't need to convert anything because the tools
can use the VMD plugins to read dcd. If the tool needs a tpr file (e.g.
carges) than you need to create one. In most cases the easiest solution to
do
Elisabeth wrote:
Dear David,
I followed your instructions and calculated Heat of vaporization of my
alkane once with one molecule in gas phase (no cutoff) and once with
equivalent number of molecules as in liquid phase as Justin suggested.
Results are as follows:
To get heat of
Elisabeth wrote:
Elisabeth wrote:
Dear David,
I followed your instructions and calculated Heat of vaporization
of my alkane once with one molecule in gas phase (no cutoff) and
once with equivalent number of molecules as in liquid phase as
Dear Justin,
I have used the same .mdp file you have used in your tutorial for
enzyme-ligand complex, I am pasting it here. My system consists of 10212
(enzyme+NADPH) atoms and 45000 water molecules.
title = Protein-ligand complex NPT equilibration
define = -DPOSRES ; position
Kishore wrote:
Dear Justin,
I have used the same .mdp file you have used in your tutorial for
enzyme-ligand complex, I am pasting it here. My system consists of 10212
(enzyme+NADPH) atoms and 45000 water molecules.
Try using the Berendsen barostat instead of P-R. Some systems don't
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