Hi All,
Any suggestions?
Thanks.
On Mon, Jan 27, 2014 at 5:01 PM, rajat desikan rajatdesi...@gmail.comwrote:
Hi All,
I am trying to calculate the angle between the axes of two alpha helices
(say A and B) in my simulation. I have separate index files for the
residues pertaining to each
That sounds strange.
Does the error happen at step? Assuming the it does occur within the
first 10 steps, here are a few things to try:
- Run cuda-memcheck mdrun -nsteps 10;
- Try running with GMX_EMULATE_GPU env. var. set? This will run the
GPU acceleration code-path, but will use CPU kernels
Does the error happen at step? Assuming the it does occur within the first 10
steps, here are a few things to try:
It happens immediately. As in:
$ time mdrun
snip
real0m3.312s
user0m6.768s
sys 0m1.968s
$
- Run cuda-memcheck mdrun -nsteps 10;
A wild backtrace appeared!
Hi
I'm desperately trying to install gromacs on Win7. I'm not very experienced.
I proceeded to install with CMake but at some point I keep giving this
error:
/
CMake Error at CMakeLists.txt:969 (message):
Linking with MKL was requested, but was not successful. The include path
to mkl.h in
On Thu, Jan 30, 2014 at 2:10 PM, AOWI (Anders Ossowicki)
a...@novozymes.com wrote:
Does the error happen at step? Assuming the it does occur within the first
10 steps, here are a few things to try:
It happens immediately. As in:
$ time mdrun
snip
real0m3.312s
user0m6.768s
sys
These are all standard in 4.6. The GPU implementation there only does
non-bonded pair interactions, which affects none of the above. The
limitation in 4.5 was that the GPU did lots more parts of the computation,
and not all kinds of algorithms are amenable to that.
Mark
On Wed, Jan 29, 2014 at
I see Bipin,
Thanks. One quick question though, am I going to change the charges to zero or
all atoms to DUM atoms for all the atoms in B state or just for the hydrogen
that will be transferred between the states (the atom where the B state was
missing before):
16 opls_270 77GLU
On Thu, Jan 30, 2014 at 4:19 PM, AOWI (Anders Ossowicki)
a...@novozymes.com wrote:
Well, with a 24k system a single iteration can be done in 2-3 ms, so those
3.3 seconds are mostly initialization and some number of steps - could be
one, ten, or even hundred.
Sure, but it fails even with
The protonated and deprotonated states will differ only in terms of
presence or absence of hydrogens, thus in B state only that hydrogen atom
which is intended to be transformed from protonated to deprotonated state
will be altered in the terms of electrostatic and vdw parameters.
On Thu, Jan
On 1/30/14, 1:57 AM, shahab shariati wrote:
Dear Justin
Thanks for your reply.
My system contains dopc lipid. ns.xtc and ns.tpr files contain all atoms
related to dopc molecule.
I want to obtain number of atoms in a first group (C38 atom in dopc) which
are located in special distance (0.74
Thank you Bipin and Justin,
As far I understand from the very informative discussion, for A state
(protonated) I will keep the charges and for B state (deprotonated) I will get
them from the unprotonated GLU topology file and paste into this one .top file.
The only difference will be the DUM
Thanks Dr. Justin for mentioning this important point.
On Thu, Jan 30, 2014 at 9:48 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/30/14, 11:12 AM, bipin singh wrote:
The protonated and deprotonated states will differ only in terms of
presence or absence of hydrogens, thus in B state only
On 1/30/14, 11:28 AM, Ozbil, Mehmet wrote:
Thank you Bipin and Justin,
As far I understand from the very informative discussion, for A state
(protonated) I will keep the charges and for B state (deprotonated) I will get
them from the unprotonated GLU topology file and paste into this one
I think so, because when I try to run grompp to create a .tpr file for the
steepest descent energy minimization it gave me these following three WARNINGS:
Generated 36 of the 36 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 36 of the 36 1-4
By the Way, My top file looks like:
[ moleculetype ]
; Namenrexcl
Protein_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
; residue 77 GLU rtp GLUH q 0.0
1 opls_900 77GLU N 1
Dear Users,
I have been doing 10 ns MD simulations of protein-ligand complexes on a
local cluster of 64 cores using GROMACS 4.5.7. However, there seems to be
no much difference in the time it takes to complete one cycle of an mdrun
(3-days - same as when I used a machine with 4 cores).
Will be
Yes it is, or should be from my experience. You need to look at the mailinglist, and it takes time t work out somethings as there also system (your simulation) dependent. Mostly these are parameters such as domain decomposition sizes, number of threads, -rdd, -rcon -dds and others (I found more
For Dummy atom, I tried to write DUM for atom type and give 0 charge but it
could not recognize the atom type. Then I just wrote the atom type with 0
charge but as I understand I could not make it a dummy atom. How can I do it?
And also for the parameters, I understand the fact that the bonding
Hello All,
I have just performed a fresh installation of gromacs version 4.6.5 on a
heterogeneous linux cluster (running centos 6.4) . After the installation I see
that the binaries, for say mdrun, work on all the machines with hardware
similar to the one on which they were installed (namely
On 1/30/14, 2:27 PM, Ozbil, Mehmet wrote:
For Dummy atom, I tried to write DUM for atom type and give 0 charge but it
could not recognize the atom type. Then I just wrote the atom type with 0
charge but as I understand I could not make it a dummy atom. How can I do it?
The DUM type has no
On Jan 30, 2014 11:57 PM, Raffaella D'Auria rdau...@ucla.edu wrote:
Hello All,
I have just performed a fresh installation of gromacs version 4.6.5 on a
heterogeneous linux cluster (running centos 6.4) . After the installation I
see that the binaries, for say mdrun, work on all the machines
Dear users,
I would like to simulate a Lennard-Jones system with one or two species of
atoms. But my knowledge is only about Lennard-Jones 6-12 potential and I
haven't figured out how to use that potential to set up the system with
GROMACS. Could anybody help me with this? Any recommended reading
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