Dear Mark,
Thank you very much for your help!
I add the restraints into my topol.top successfully!
But there is still two questions:
(1) After [angle_restraints] is added into my .top file, should I write
additional parameters into .mdp file to run
angle restraints? Because after
Following your advice I compiled gromacs with DGMX_CPU_ACCELERATION=SSE4.1
and now it is working :) . Thanks a lot
- Vishal
Undergraduate Student
Department of Chemistry
Indian Institute of Technology Guwahati
On Tue, May 21, 2013 at 7:45 AM, Justin Lemkul jalem...@vt.edu wrote:
On 5/20/13
Dear Gromacs users,
I am trying to simulate a large systems embeded in a membrane (roughly
360,000 atoms). I would like to equilibrate it at 300K and 1 atm. To this
mean, I use simulated annealing to slowly warm up the system from 50 to
300K, under NPT conditions.
For the simulation, I use
On 5/21/13 5:41 AM, Vishal Kumar Jaiswal wrote:
Following your advice I compiled gromacs with DGMX_CPU_ACCELERATION=SSE4.1
and now it is working :) . Thanks a lot
I suggested this as a diagnostic measure (not a fix), and it is good that it is
working properly, but is also indicative of a
On 5/21/13 7:55 AM, Baptiste Demoulin wrote:
Dear Gromacs users,
I am trying to simulate a large systems embeded in a membrane (roughly
360,000 atoms). I would like to equilibrate it at 300K and 1 atm. To this
mean, I use simulated annealing to slowly warm up the system from 50 to
300K, under
Thank your for your answer !
Actually yes, annealing is just a preparatory step, so I'll just keep
Berendsen barostat for the equilibration. I was just wondering about the
behaviour of Parrinello-Rahman. Thanks !
Baptiste
2013/5/21 Justin Lemkul jalem...@vt.edu
On 5/21/13 7:55 AM, Baptiste
http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49002 looks like it might be
the issue - fixed between gcc 4.6.1 and 4.6.2. If Vishal would like to
update his gcc to the latest version (which we always recommend, because
such issues are distressingly frequent), then he should be able to take
advantage
I've opened http://redmine.gromacs.org/issues/1259 to discuss this issue.
All users are warned that such issues are possible, and if you don't run
the regression test suite, you can be at the mercy of a buggy compiler!
Mark
On Tue, May 21, 2013 at 2:35 PM, Mark Abraham
On Tue, May 21, 2013 at 11:31 AM, jnsong jns...@itcs.ecnu.edu.cn wrote:
Dear Mark,
Thank you very much for your help!
I add the restraints into my topol.top successfully!
But there is still two questions:
(1) After [angle_restraints] is added into my .top file, should I write
additional
Hi, all,
I performed some NPT simulations. I want to plot the density change,
for one single time step or averaged over time, along some direction,
such as x direction or y direction.
I wonder how I can do that with the output files.
It will be much better if it can be done separately for a
Dear Gromacs users,
How to define distance restraints between two molecules(protein and a lipid)
in a topology file.
Thanks..
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View this message in context:
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I am working on some specific features of Cray compiler.
But it seems like other features are also necessary.
Thanks a lot for the patch.
On Mon, May 20, 2013 at 6:48 PM, Roland Schulz rol...@utk.edu wrote:
Hi,
I agree with Mark that it is probably not worth it. Why are you
interested in
You can't - the atoms must be part of the same [moleculetype]. The good
news is that a [moleculetype] can have whatever you want in it, so you can
have more than one molecule. The bad news is that you'll have to be cunning
with renumbering atoms in the merged [moleculetype] and there's no tools
The energy files contain the box vectors when that is not constant, so
g_energy will be your friend.
Mark
On Tue, May 21, 2013 at 4:11 PM, Bao Kai paeanb...@gmail.com wrote:
Hi, all,
I performed some NPT simulations. I want to plot the density change,
for one single time step or averaged
Hi Mark,
Is there anyway to define NMR distance restraints in MD simulations to do
refinement for the complex structure.
On Tue, May 21, 2013 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
You can't - the atoms must be part of the same [moleculetype]. The good
news is that a
Yes. Check out the manual first!
Mark
On Tue, May 21, 2013 at 5:16 PM, Rama Krishna Koppisetti
ramkishn...@gmail.com wrote:
Hi Mark,
Is there anyway to define NMR distance restraints in MD simulations to do
refinement for the complex structure.
On Tue, May 21, 2013 at 10:11 AM, Mark
Hi..,Mark
but it is within the same molecule , not in inter-molecules.
On Tue, May 21, 2013 at 11:36 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
Yes. Check out the manual first!
Mark
On Tue, May 21, 2013 at 5:16 PM, Rama Krishna Koppisetti
ramkishn...@gmail.com wrote:
Hi Mark,
On 5/21/13 12:53 PM, Rama Krishna Koppisetti wrote:
Hi..,Mark
but it is within the same molecule , not in inter-molecules.
That's what distance restraints are designed for. Please refer to the manual
for topology syntax and explanation of the relevant parameters.
-Justin
On Tue,
Hello. I have a cluster (12 nodes, 24 cores on each). Also I've compiled
mdrun with MPI.
Now when I try to run a MD on this cluster, it takes near 20 hours to
complete. But when I try the same simulation on a PC with 8 cores, it takes
near 10 hours to complete. I thought that it will take less on
Hi,
Thank you for your response.
I guess I took the problem wrong. I guess I need a topology file for decane.
I did some google search, generally people told that it can be done
manually, while this is really not my field. My field is CFD, while
my boss gave me some molecular simulation
On 5/21/13 1:15 PM, Андрей Гончар wrote:
Hello. I have a cluster (12 nodes, 24 cores on each). Also I've compiled
mdrun with MPI.
Now when I try to run a MD on this cluster, it takes near 20 hours to
complete. But when I try the same simulation on a PC with 8 cores, it takes
near 10 hours to
virtualchemistry.org has some topology files for many organic liquids.
Regards
Rajesh
On Tue, May 21, 2013 at 1:21 PM, Bao Kai paeanb...@gmail.com wrote:
Hi,
Thank you for your response.
I guess I took the problem wrong. I guess I need a topology file for
decane.
I did some google
Hi, Rejesh,
Thanks for the reply.
Unfortunately, they does not have the topology file for decane.
Best Regards,
Kai
virtualchemistry.org has some topology files for many organic liquids.
Regards
Rajesh
On Tue, May 21, 2013 at 1:21 PM, Bao Kai paeanball at gmail.com wrote:
Hi,
Thank you
Yes, I'm using all cores. All nodes are connected by Ethernet. Now I see
that when I change number of processes or number of threads per node I can
change mdrun performance. But I think it is still too slow. Is there a way
to speed up mdrun on cluster? Some specific settongs or so? Sorry for my
On 5/21/13 2:58 PM, Андрей Гончар wrote:
Yes, I'm using all cores. All nodes are connected by Ethernet. Now I see
that when I change number of processes or number of threads per node I can
change mdrun performance. But I think it is still too slow. Is there a way
to speed up mdrun on cluster?
On 5/21/13 1:44 PM, Bao Kai wrote:
Hi, Rejesh,
Thanks for the reply.
Unfortunately, they does not have the topology file for decane.
For a simple molecule like decane, g_x2top can probably create a reasonable
topology for you.
-Justin
virtualchemistry.org has some topology files for
Dear Sir,
I performed another round of trial with different set of temperature and I
got the avg accp. ration around 0.22. Here's the temp. dist. that I used :
250 268 288 308 331 355 380 408 438 469 503 540 579 621
I then checked the replica_index and replica_temp files for each replica
Hello gromacs users
I performed a 1 ns simulation of N-isopropylamide in water. Now i wish to
calculate the average no of water molecules(averaged over entire
trajectory) within a certain distance of solute and no. of water molecules
that form H-bonds with solute.
Could you guide me as to what
The BAR method calculates a ratio of weighted average of the Hamiltonian
difference of state B given state A and vice versa.
So, for different peptides, can this method apply to compare the stability
of peptides?
Thank you very much!
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Hi all,
I've been running 5fs timestep simulations successfully without gpus
(united-atom, HEAVYH). When continuing the same simulations on a gpu cluster
utilising the verlet cutoff-scheme they crash within 20 steps. Reducing the
timestep to 2fs runs smoothly, however I noticed the message:
Sorry guys, I used the raw text field to make the message easier to read and
noticed it didn't come through on the email.
If you view it on the user forum you can see the note and mdp file.
The note was:
For optimal performance with a GPU nstlist (now 10) should be larger.
The optimum depends on
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