Hello all,
Now I want to have a simulation of water and methane system, but when I wrote a
methane.itp and the force field file, it could not run correctly. I used tip4p
water and the opls-aa methane. According to the simulation with NPT, not only
the pure methane system, but also the water and
Hello everyone,
I am new to using gromacs. I am currently studying an enzyme catalysing a
transfer reaction. there are two substrates and I want to restraint
specific interactions between different parts of the ligands and the
protein. As I understand so far from reading various discussions in
Hi Chandan
Are you using the same version of GCC compiler that you used to compile
CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think there
was some kind of incompatibility between the two).
Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This
worked in my
Hi,
The code compiled, so the compiler is not the issue.
I guess mdrun picked up GPU 0, which it should have ignored. You only want to
use GPU 1.
Could you try running:
mdrun -ntmpi 1 -gpu_id 1
Cheers,
berk
Date: Thu, 28 Mar 2013 10:51:58 +0200
Subject: Re: [gmx-users] no CUDA-capable
p{margin:0;padding:0;}
Dear Justin,
Thank for your pointing out my issues. I just want to know how it can be
converted.
I have referred the equation in chapter 4 and do not know exactly how I use
them.
For example, The C-O bond distance and force constant written as (0.112 and
On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess g...@hotmail.com wrote:
Hi,
The code compiled, so the compiler is not the issue.
I guess mdrun picked up GPU 0, which it should have ignored. You only want
to use GPU 1.
Could you try running:
mdrun -ntmpi 1 -gpu_id 1
$mdrun_461 -ntmpi 1
Hi,
I am not the expert on GPU detection, so we'll need to wait until an expert
replies.
Maybe GPU 0 is ignored and the GPUs are renumbered, could you try:
mdrun -ntmpi 1 -gpu_id 0
Also your tpr file is from an older version. It will not run on a GPU.
You need to set the mdp option:
Dear users,
This time, I calculated the diffusion coefficients of protein for each 10
ns of the simulation providing a total simulation time of 200 ns.
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
-endfit -1 -b 0 -e 1
g_msd -f traj.xtc -s topol.top -o msd2.xvg
On 2013-03-28 10:40, Ahmet yıldırım wrote:
Dear users,
This time, I calculated the diffusion coefficients of protein for each 10
ns of the simulation providing a total simulation time of 200 ns.
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
-endfit -1 -b 0 -e 1
g_msd
Does that mean the atoms will shrink and adjust at the time inflategro step
and
this closely packed lipids will stay apart? Because as you said the energy
of course will be high on selected atoms during first EM step.
Could you suggest me that, can I proceed as such with my system, since
Hi,
If mdrun says that it could not detect GPUs it simply means that the GPU
enumeration found no GPUs, otherwise it would have printed what was found.
This is rather strange because mdrun uses the same mechanism the
deviceQuery SDK example. I really don't have a good idea what could be the
The easiest solution would be using 'pull_geometry = distance' in all
three dimensions. Then you can be sure that both groups are pulled
together. Small remark: One group would be fixed for the pulling, and
the second group gets pulled towards the first group. So if you want to
have both
On Thu, Mar 28, 2013 at 4:09 PM, Szilárd Páll szilard.p...@cbr.su.sewrote:
Hi,
If mdrun says that it could not detect GPUs it simply means that the GPU
enumeration found no GPUs, otherwise it would have printed what was found.
This is rather strange because mdrun uses the same mechanism the
Dear Prof.Spoel,
if I do as you said, I will get only one diffusion coefficient. I want to
calculate one diffusion coefficient for each 10
ns of the simulation time of 200 ns. That is, I want to get 20 diffusion
values.
2013/3/28 David van der Spoel sp...@xray.bmc.uu.se
On 2013-03-28 10:40,
Hi !!
I problem with the permission of /dev/nvidia*
changed it to 0666 /dev/nvidia*
Everything resolved. mdrun can be executed as normal user.
Thanks everyone.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Thu, Mar 28, 2013 at 4:26 PM, Chandan Choudhury iitd...@gmail.comwrote:
On 3/28/13 6:38 AM, Dr. Vitaly Chaban wrote:
Does that mean the atoms will shrink and adjust at the time inflategro step
and
this closely packed lipids will stay apart? Because as you said the energy
of course will be high on selected atoms during first EM step.
Could you suggest me that, can
On 3/27/13 11:32 PM, sdshine wrote:
Dear all,
Does that mean the atoms will shrink and adjust at the time inflategro step
and
this closely packed lipids will stay apart? Because as you said the energy
of course will be high on selected atoms during first EM step.
Could you suggest me that,
On 3/28/13 5:18 AM, 라지브간디 wrote:
p{margin:0;padding:0;}
Dear Justin,
Thank for your pointing out my issues. I just want to know how it can be
converted.
I have referred the equation in chapter 4 and do not know exactly how I use
them.
For example, The C-O bond distance and force
On 3/28/13 4:01 AM, Saravanan wrote:
Hello everyone,
I am new to using gromacs. I am currently studying an enzyme catalysing a
transfer reaction. there are two substrates and I want to restraint
specific interactions between different parts of the ligands and the
protein. As I understand so
On 3/27/13 5:12 PM, Peter Eastman wrote:
I'm implementing a TOP file reader, and I have a question about an ambiguity in
the format. The [ pairs ] block lists atom pairs that should be handled
specially (exclusions and 1-4 interactions). In addition, the gen-pairs flag
can indicate that
if I do as you said, I will get only one diffusion coefficient. I want to
calculate one diffusion coefficient for each 10
ns of the simulation time of 200 ns. That is, I want to get 20 diffusion
values.
2013/3/28 David van der Spoel sp...@xray.bmc.uu.se
On 2013-03-28 10:40, Ahmet yıldırım
Thank you.. I hoped it would be simpler. how do I go about creating unified
protein-ligand [moleculartype] directives. Can you suggest any material
available on this topic? that would be extremely helpful.
-Saravanan
On 28 March 2013 16:45, Justin Lemkul jalem...@vt.edu wrote:
On 3/28/13
On Thu, Mar 28, 2013 at 8:18 AM, Saravanan msrvnn+...@gmail.com wrote:
Thank you.. I hoped it would be simpler. how do I go about creating unified
protein-ligand [moleculartype] directives. Can you suggest any material
available on this topic? that would be extremely helpful.
Depending on
Dear users,
Again, I have strange results (for 10,50,100,150,200 ns). I am wondering,
is there a bug with g_msd?
Commands for trestart to 20 ps:
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
-endfit -1 -b 0 -e 1
g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20
perhaps, you could make a plot??
it is difficult to understand what you are speaking about.
Dr. Vitaly Chaban
On Thu, Mar 28, 2013 at 2:59 PM, Ahmet yıldırım ahmedo...@gmail.com wrote:
Dear users,
Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is
there a bug
On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com wrote:
Dear users,
Again, I have strange results (for 10,50,100,150,200 ns). I am wondering,
is there a bug with g_msd?
I see no evidence for a bug, and you should avoid such speculation unless
you know exactly how the
Dear GMX-Users
I have a problem while trying to insert a drug molecule into my simulation.
I have the topology file generated from the ATB-server. And accordingly I
have edited the aminoacid.rtp ffbonded.itp file. I have transcribed the
forcefield parameters into GROMOS96 format. here is my .itp
Hi Justin,
So if I understand you correctly, there are actually three different ways the
parameters can be specified. In order of decreasing precedence:
1. If there's a [pairs] line and it includes parameters, use those parameters.
2. If there's a [pairs] line and it doesn't include
Dear gmx,
I would like to set virtual sites for CO molecules with some specific charge.
As per GROMACS manual, I've created virtual site2 in topology file for CO.
Also, given the information in .rtp file as well as added the COM(center of
mass) atom in .gro file. However, when I use gromp, it
Hi dear All!
Good day dear forum! I have a question abour freezing of atoms during MD.
The idea is that - I have a protein and one domain contains a site. Also I
have two ligands, one of them is better inhibitor in comparison with
another one. To prepare the topology of the inhibitor I need to use
Please see plot:
http://imageshack.us/photo/my-images/35/diffusion.png/
2013/3/28 Justin Lemkul jalem...@vt.edu
On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com
wrote:
Dear users,
Again, I have strange results (for 10,50,100,150,200 ns). I am wondering,
is there a
Hi,
I'm glad that it got figured out. For all those who might be wondering what
exactly are you referring to here is a quick summary.
The NVIDIA driver needs /dev entries to be present for the GPU devices in
use and these entries need the right permissions in order to allow
user-space programs
3. If gen-pairs is yes, then generate parameters for all 1-2, 1-3, and 1-4
pairs for which we did not already find parameters in step 1 or 2 (regardless
of whether or not a [pairs] line exists for a particular pair).
Or rather, generate an [exclusions] record for each 1-2 and 1-3, and a
The simplest advice is to increase sampling.
Please see plot:
http://imageshack.us/photo/my-images/35/diffusion.png/
2013/3/28 Justin Lemkul jalem...@vt.edu
On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com
wrote:
Dear users,
Again, I have strange results
After further study of the documentation, I find myself getting more confused
rather than less. I see that the [pairs] and [pairtypes] directives only
specify LJ parameters, not Coulomb parameters. (There's a function type 2 for
[pairs] that does include charges, but the manual says that
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
On 3/28/13 7:14 PM, Peter Eastman wrote:
3. If gen-pairs is yes, then generate parameters for all 1-2, 1-3, and 1-4
pairs for which we did not already find parameters in step 1 or 2 (regardless of whether
or not a [pairs] line exists for a particular pair).
Or rather, generate an
On 3/28/13 8:25 PM, Peter Eastman wrote:
After further study of the documentation, I find myself getting more confused rather than
less. I see that the [pairs] and [pairtypes] directives only specify LJ parameters, not
Coulomb parameters. (There's a function type 2 for [pairs] that does
On 3/28/13 5:32 PM, Ahmet yıldırım wrote:
Please see plot:
http://imageshack.us/photo/my-images/35/diffusion.png/
How did you come up with your expected values? What does the original msd.xvg
plot look like? It should be basically linear. If it's not, then you have
found the source of
On 3/28/13 7:56 PM, Dr. Vitaly Chaban wrote:
The simplest advice is to increase sampling.
I think the OP needs to describe what the system is in greater detail. For a
simple liquid, I would opine that 200 ns is normally vast overkill. For a
membrane, it may not be enough. There's just
Thank you, Berk, Justin, and Matthew, for your assistance.
I checked with my sysadmin, who said:
The /global/scratch FS is Lustre. It is fully POSIX and the fsync etc
are fully and well implemented. However when the 'power off' command is
issued there is no way OS can finish I/O in a
On 3/28/13 4:24 PM, Алексей Раевский wrote:
Hi dear All!
Good day dear forum! I have a question abour freezing of atoms during MD.
The idea is that - I have a protein and one domain contains a site. Also I
have two ligands, one of them is better inhibitor in comparison with
another one. To
42 matches
Mail list logo
