On 21/02/2012 19:02, "David van der Spoel" wrote:
> On 2/21/12 6:17 PM, Richard Broadbent wrote:
>> Dear All,
>>
>> I am considering conducting a simulation of a polymeric system in
>> gromacs. I would like to use the COMPASS forcefield as it has a complete
>> parameter set for my molecule.
>
Dear Cat,
> Dear experts,
>
> I am trying to do the following command:
>
> /usr/local/gromacs/bin/g_covar_d -s test.pdb -f test.mdcrd -o -v
>
If you are using -o & -v options you should specify files for them
> But the following error message is found:
>
>
Dear Marcelo,
I think you need to calm down. You are using a very nice piece of free code
which has in excellent documentation as well as being open source.
If you are using a piece of software in a non-standard way it stands to reason
that it might not be documented. When this occurs in my re
Dear Silard,
cmake -DGMX_CPU_ACCELERATION=AVX_256 -DGMX_DEFAULT_SUFFIX=OFF
-DGMX_BINARY_SUFFIX="_avx" -DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_DOUBLE=ON
-DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl
-DMKL_INCLUDE_DIR=$MKLROOT/include
-DMKL_LIBRARIES="$MKLROOT/lib/intel64/libmkl_core.
Dear Steven,
There is no universal method to do this and many people spend years
studying the various techniques. However,
http://pubs.acs.org/doi/abs/10.1021/ct900369w gives an overview of some of
the most widespread techniques used and its references will provide
further details. Futhermore, the
Dear Rajiv,
Without a clear explanation of what you are doing and the specific error
message from grompp it is impossible to offer any sensible advice.
Other pieces of information which might be useful would be, the topology
file, the actual grompp line, and the gro file for a single CO molecule
Dear Rajiv,
The .itp looks fine to me except for the coefficient in the virtual site
which I think should be much closer to 0.5.
If the issue is that you don't have the coordinate on the COM in your .gro
file then you will need to generate it yourself. If you have one CO
molecule which you use to
Please include the full error message and the grompp line you used when
asking for help. Without them I can't tell what you are doing.
Richard
On 04/04/2013 17:40, "라지브간디" wrote:
>
>Dear Richard,
>
>I've included the COM in my .gro and also updated the rtp, atp and
>ffnonbonded.itp files as wel
On 11/04/2013 11:17, "manara r. (rm16g09)" wrote:
>Dear gmx-users,
>
>I am having a problem with a periodic molecule and the domain
>decomposition, I wish to use a high number of processors (circa 180, but
>can obviously be reduced) and therefore need to use the -rdd or -dds
>flags (I believe),
On 12/04/2013 21:50, "Jesper Sørensen" wrote:
>Hi Berk and others,
>
>Sorry it has been a long time since this issue was posted, but I got
>side-tracked from this issue with other projects. And I want to make sure
>I understand this correctly before venturing into more simulations. So
>this get
On 13/05/2013 08:46, "Sainitin Donakonda" wrote:
>Hello,
>
>I am trying to run 20 ns protein ligand simulation on cluster using
>following MD.MDP file
>
>; 7.3.3 Run Control
>integrator = md; leap-frog integrator
>dt = 0.002
I've been running on my Universities GPU nodes these are one E5-xeon (6-cores
12 threads) and have 4 Nvidia 690gtx's. My system is 93 000 atoms of DMF under
NVE. The performance has been a little disappointing ~10ns/day. On my home
system using a core i5-2500 and a nvidia 560ti I get 5.4ns/day
The conversion is in ffnonbonded.itp. However, unless you plan to modify
the forcefield you shouldn't need this.
Richard
On 01/06/2013 00:57, "Hari Pandey" wrote:
>Dear Gromacs users,
>
>I am a new user and I have some questions
> I confused about indexing. in atomtypes.atp clearly we can kn
Dear Thomas,
Whilst in principle a constraint should do what you are asking, you might be
better off using multiple vsites to solve the problem so that there is an
algebraic as apposed to numerical mapping of the forces. My immediate
thought is to use two type 3 (or if necessary type 3fd) virtual
An Angle constraint amounts to fixing a triangle. To do this you need to
constrain the distances between all the atoms as you know the of the bonds
6064, 6063 and 6063, 6065 and the angle between the two bonds it is a
trivial geometry problem calculate the length of the third side of the
triangle (
Virtual sites are by definition have no mass.
If you simply ignore the mass of the carbon the molecule will be too light
and its translational momentum will therefore be too small meaning it will
move too quickly.
If you place half the mass of the carbon on each oxygen the moment of
inertia will
As these are binary files the formatting can be quite complex I would
suggest using the library available here:
http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
This includes all the functions necessary to read/write these formats and is
licensed under LGPL.
Richard
On 13/08
Dear Arman,
I've noticed a similar effect where large voids appear in a solvent when
running long nose-hoover NVT simulations. I have checked and it is not a pbc
artefact.
I found that if I turn the thermostat off the holes go away. I've also found
that reducing the number of cores removes the hol
I wish to keep certain parts of the backbone of my polymer rigid and planar,
as my primary interest is in the long length and timescale motion of the
polymer.
I am attempting to utilise virtual sites as a means to keep aromatic groups
rigid and planar. My intention is to replace groups such as p
>
> Any particular reason why improper dihedrals would not be suitable? They are
> significantly easier to implement.
Yes the force field parameters for the molecule are not known and I am
therefore fitting the parameters to Density Functional Theory. If I allow
the units to move out of plane eve
Have you thought about using the cross product. If you took the cross product
of the unit vector in the direction of every atom starting from atom 1 then
moved on to starting from atom 2 and so on you would have a set of vectors
normal to every group of three atoms. If you then normalised them
Hi Sanku
The ^M ‘s in that sample indicate a line break that was issued by a different
text formatting standard. This frequently happens if files are generated in one
OS say Windows then viewed in another say unix. Is your version of gromacs
compiled for your system or was is compiled for a dif
For my system reducing shake-tol greatly improves the energy conservation
generally 1.0e-7 is the largest I would use. However if you want very good
energy conservation 1.0e-9 or lower might be needed.
This effect might only be for my system but I think it might help here too
Richard
On 25/06/20
23 matches
Mail list logo
