Thanks for the clarification.
On Thu, Apr 25, 2013 at 7:48 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/25/13 9:48 AM, Richard Broadbent wrote:
The 4.6.1 release is a more advanced version of gromacs with the latest
kernels
and features (GPU support, verlet cut-offs etc.).
4.5.7 is a
Thanks for your reply.
On Thu, Apr 25, 2013 at 7:18 PM, Richard Broadbent
richard.broadben...@imperial.ac.uk wrote:
The 4.6.1 release is a more advanced version of gromacs with the latest
kernels and features (GPU support, verlet cut-offs etc.).
4.5.7 is a maintenance release for those of
On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl wrote:
Thanks for the answer. I'll check gmx4.5.7 and report back.
I am not sure what you mean by GROMACS swaps the coordinates not the
ensemble data. The coupling to P and T and not exchanged with it?
The code in
Dear Gromacs users,
I am trying to compute the free energy of hydration of ethane in order to get
more familiar with the implementation of expanded ensemble in Gromacs v. 4.6.1.
The simulations runs fine and the balancing/weight factors are equilibrated
after around 1.6 ns (a short
Dear Gromacs Users and Developers,
I am doing do_dssp analyses using a trajectory and structure file both in
pdb format.
My trajectory is 1 microseconds (with snapshots saved every 10 ps), xpm2ps
doesn't show ticks on X-axis. I get following message:
Auto-tick spacing failed for X-axis, guessing
Dear Justin,
Thanks for your response and the perfect tutorial. I found the details
I needed in it.
Best regards,
Sarah
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Average coordinates are problematic and not generally representative. Consider
for instance the average coordinates of a methyl group connected to X. The
rotation around the C-X bond causes the average positions of the hydrogens to
line up. Consider using g_cluster to find representative
Dear Sir,
Thanks for the useful insight.
On Fri, Apr 26, 2013 at 2:21 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Average coordinates are problematic and not generally representative.
Consider for instance the average coordinates of a methyl group connected
to X. The rotation around the
Dear Users,
I am running my puling simulations of ligand with constant velocity. First
I minimize and equilibrate my system:
grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
mdrun -s em.tpr -deffnm em
grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
mdrun -s
Hi Xavier,
I used a dt of 10 ps with nstlist of 2. In that case the Temp of the system is
stable and the energy well conserved (400 ns of run). I do know if it is
optimal but it works for my system.
Stephane
--
Message:
TL;DR version (longer version below):
Due to the stochastic nature of SMD (and pulling experiments in general)
it is quite natural that the results for different simulations will not
be excatly the same.
I would say you are fine. Thing is, if you do ligand unbinding SMD
simulations the
nstlist of 2 is a be extreme! Did you try 5! It should be fine … but if your
are happy that's ok :))
On Apr 26, 2013, at 12:37 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote:
Hi Xavier,
I used a dt of 10 ps with nstlist of 2. In that case the Temp of the system
is stable and the
On 4/26/13 4:33 AM, Neha Gandhi wrote:
Dear Gromacs Users and Developers,
I am doing do_dssp analyses using a trajectory and structure file both in
pdb format.
My trajectory is 1 microseconds (with snapshots saved every 10 ps), xpm2ps
doesn't show ticks on X-axis. I get following message:
Think i now understand your question. Forget what i wrote before.
I could imagine the the 'grompp -t npt.cpt' part is a problem.
If the simulations would be numerical reproducible, one should get the
same results. As they are not, the results will differ somewhat (would
think the more, the
Thanks for this. I think option 2 is more reasonable. However, still do not
know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
simulations...
On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier schl...@uni-mainz.dewrote:
Think i now understand your question. Forget what i
hey thanks alot..got it :)
-
thanks in advance :)
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Don't know. One idea i have: Take a flexible and a relative rigid system
and perform simulations with the same starting conditions (- using -t
*.cpt). I would imagine that for the flexible system the trajectories
start earlier to deviate, since more stuff could happen (system is more
flexible
Xavier,
as i said in my message, this nstlist value is not optimal, but it works !!! if
wlll try a higher nstlist value, if I have same problem in futur simulations
Thanks again for you help
Stephane
Hello all,
I ran 10ns molecular dynamics simulation of protein ligand complex ..in
which protein homology model..finally i analyzed .xtc file which is
produced after MD production run..first i plotted RMSD profile of backbone
of the protein ..it show that line starts from 0.2 nm to 0.4 nm and
On 4/26/13 9:33 AM, Sainitin Donakonda wrote:
Hello all,
I ran 10ns molecular dynamics simulation of protein ligand complex ..in
which protein homology model..finally i analyzed .xtc file which is
produced after MD production run..first i plotted RMSD profile of backbone
of the protein ..it
I am not sure but different force profiles may be due to the
non-equilibrium relaxation problem. The path on the energy landscape during
the non-equilibrium simulations depends on the pulling rate and/or
relaxation of any unknown coordinates correlated with pulling coordinates.
If during pulling,
there should be an extra option in your mdrun command line if
reproducibility is an issue:
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
the value of -reprod is set to no by default, turn on that option and
trajectories should be the same.
best
Andre
Hi all,
I am going to use 4.6 version of gmx on GPU. I am not sure of the mdrun
command though. I used to use mpirun -np 4 mdrun_mpi -deffnm .. in 4.5.4.
Can I use the same command line as before for mdrun or other tools?
Thank you very much,
--
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Hello
Doe anybody know what is the best (the most suitable) set of parameters
to use for ATP/Mg+2 ?
I have seen from the literature that people have used mainly either the
CHARMM27 parameters or the ones in
Meagher KL, Redman LT, Carlson HA (2003) Development of polyphosphate
parameters for use
On 4/26/13 10:50 AM, Juliette N. wrote:
Hi all,
I am going to use 4.6 version of gmx on GPU. I am not sure of the mdrun
command though. I used to use mpirun -np 4 mdrun_mpi -deffnm .. in 4.5.4.
Can I use the same command line as before for mdrun or other tools?
Please read through the
Hi,
I am trying to calculate ligand binding affinity of Dimeric Protein(198
residues) complexed with a peptide(3 residues) using Linear Interaction
Energy method.The water box dimensions of ligand with protein and Ligand
in water are considered to be same.
I am encountering problem in
Dear Mark Junghans,
I have got it. There is some problem in the Makefile. Thanks for your
suggestions and help
On Fri, Apr 26, 2013 at 11:12 AM, Venkat Reddy venkat...@gmail.com wrote:
Dear Mark Junghans,
Thanks for your valuable suggestions.
I have gone through the README file. It says
Dear:
I've installed gromacs-4.6.1 in a GPU workstation with two GTX690.
Here is my step:
./configure --prefix=/home/albert/install/openmpi-1.4.5 CC=icc CXX=icpc
F77=ifort FC=ifort
make
make install
cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF
You got a warning at configure-time that the nvcc host compiler can't
be set because the mpi compiler wrapper are used. Because of this,
nvcc is using gcc to compile CPU code whick chokes on the icc flags.
You can:
- set CUDA_HOST_COMPILER to the mpicc backend, i.e. icc or
- let cmake detect MPI
IC.
it works very well now.
thanks a lot
Albert
On 04/26/2013 08:01 PM, Szilárd Páll wrote:
You got a warning at configure-time that the nvcc host compiler can't
be set because the mpi compiler wrapper are used. Because of this,
nvcc is using gcc to compile CPU code whick chokes on the icc
Dear:
I've got two GTX690 in a a workstation and I found that when I run the
md production with following two command:
mpirun -np 4 md_run_mpi
or
mpirun -np 2 md_run_mpi
the efficiency are the same. I notice that gromacs can detect 4 GPU
(probably because GTX690 have two core..):
4
Hello:
I am going to run gromacs with command:
mpirun -np 4 mdrun_mpi -s em.tpr -c em.gro -v -g em.log -gpu_id #0, #2,
#3, #4
but it failed with messages:
Program mdrun_mpi, VERSION 4.6.1
Source code file:
/home/albert/install/source/gromacs-4.6.1/src/gmxlib/statutil.c, line: 364
Fatal
Hi All,
I just read the paper pertaining to Gromos 54A8. I was wondering if the
force field files were available somewhere?
Thanks.
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On 4/26/13 3:37 PM, Albert wrote:
Hello:
I am going to run gromacs with command:
mpirun -np 4 mdrun_mpi -s em.tpr -c em.gro -v -g em.log -gpu_id #0, #2, #3, #4
but it failed with messages:
Program mdrun_mpi, VERSION 4.6.1
Source code file:
On 4/26/13 3:58 PM, Rajat Desikan wrote:
Hi All,
I just read the paper pertaining to Gromos 54A8. I was wondering if the
force field files were available somewhere?
ATB is usually a good source for Gromos96 parameter sets:
http://compbio.biosci.uq.edu.au/atb/
The latest they have is 54A7,
If the corrupted frame is at 1000 ps, and you can not get at the data after the
corrupted frame by using:
trjconv -b 1100 , then I suspect that you don't have any good solution here,
unless the developers put in
some type of magic number at the start of each frame that you could search for
with
Dear all:
I was using the MFFA version of Gromacs which is provided by m.j.louhivuori at
http://md.chem.rug.nl/~mara/mffa.html.
I have some quesition about this version:
i.I saw the implementation of MFFA always with the flip-flop of lipid.Can I
apply the flip-flop with this MFFA version of
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