Liu, Liang wrote:
Thanks. Actually I applied just because the tutorial said so :(
What I need is the structures only, I googled, but did not obtain useful
information about Gromacs with REMD. Maybe I need to read the manual
again :(
What structure(s)? The .xtc files contain the coordina
Thanks. Actually I applied just because the tutorial said so :(
What I need is the structures only, I googled, but did not obtain useful
information about Gromacs with REMD. Maybe I need to read the manual again
:(
I am totally fresh to MD simulation, just worked on this for 1 week ...
On Thu, S
On 30/09/2011 2:50 AM, Liu, Liang wrote:
After running for more than 12 hours, the REMD simulation is completed
and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files.
Yep. One for each simulation.
Not sure if the result is reasonable.
Justin told you yesterday they would not be, because
After running for more than 12 hours, the REMD simulation is completed and
what I get is 50 log, 50 trr, 50 cpt and 50 tpr files.
Not sure if the result is reasonable.
I tried to analyze the result, and after applying demux.pl, two
files replica_index.xvg replica_temp.xvg are obtained.
My questi
After running for more than 12 hours, the REMD simulation is completed and
what I get is 50 log, 50 trr, 50 cpt and 50 tpr files.
Not sure if the result is reasonable.
I tried to analyze the result, and after applying demux.pl, two
files replica_index.xvg replica_temp.xvg are obtained.
My questi
Am Do, 29.09.2011, 01:38 schrieb Mark Abraham:
> If the MPI configuration allows physical processors to be
> over-allocated, then GROMACS is none the wiser.
Over-allocation is the default in Open MPI[1]. So it's technically
possible to run 50 MPI processes on 2 cores. Whether or not this is a good
Not know. I will update the result tomorrow, as the 5 steps take really
long time :(
On Wed, Sep 28, 2011 at 4:38 PM, Mark Abraham wrote:
> On 29/09/2011 7:20 AM, Justin A. Lemkul wrote:
>
>>
>>
>> Liu, Liang wrote:
>>
>>> Yes, they are updated like:
>>> ...
>>> Replica exchange at step 5700
On 29/09/2011 7:20 AM, Justin A. Lemkul wrote:
Liu, Liang wrote:
Yes, they are updated like:
...
Replica exchange at step 5700 time 11.4
Repl ex 01 x 23 x 45 x 6789 x 10 11 x
12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x
26 27 28 29
Liu, Liang wrote:
Yes, they are updated like:
...
Replica exchange at step 5700 time 11.4
Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12
13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27
28 29 x 30 31 32 33 x 34 35 36 37 x 38
Yes, they are updated like:
...
Replica exchange at step 5700 time 11.4
Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12 13
14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 28
29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 43 x
4
Liu, Liang wrote:
Thanks. currently what I see is the program runs very slowly, but get
.log file for all the 50 replicas, does this mean all of them are running?
Are the log files being updated, or do they all simply contain a fatal error
message that there are insufficient nodes? I cann
Thanks. currently what I see is the program runs very slowly, but get .log
file for all the 50 replicas, does this mean all of them are running?
On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> Well, although this makes sense, why all the 50 replicas are runn
Liu, Liang wrote:
Well, although this makes sense, why all the 50 replicas are running
when I run "mpirun
-np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on my own
computer with only 2 cores?
I can offer no explanation for this behavior, but I expect that either not all
of them ar
Well, although this makes sense, why all the 50 replicas are running when I
run "mpirun
-np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on my own computer
with only 2 cores?
By the way, would you please show me where I can find the reasonable replex
number information in the literature? I
Liu, Liang wrote:
So if my personal computer have 2 cores, the np should be set to 2? Does
it relate to -multi?
That means you can only run 2 replicates. Bad idea. You'll need access to a
much better cluster to do anything meaningful. All REMD simulations have to be
run simultaneously.
So if my personal computer have 2 cores, the np should be set to 2? Does it
relate to -multi?
How to choose a reasonable number for -replex? the smaller the better?
Thanks again.
On Wed, Sep 28, 2011 at 3:06 PM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> This works. Thanks a lot.
>>
Liu, Liang wrote:
This works. Thanks a lot.
Currently I am running on an RNA molecule and I want to a 1 ns REMD
simulations with 50 temperatures,
would you please have a look at the following command "mpirun -np 50
mdrun_mpi -s md.tpr -multi 50 -replex 50". Is this right?
How to choose the
This works. Thanks a lot.
Currently I am running on an RNA molecule and I want to a 1 ns REMD
simulations with 50 temperatures,
would you please have a look at the following command "mpirun -np 50
mdrun_mpi -s md.tpr -multi 50 -replex 50". Is this right?
How to choose the numbers for np, multi or
Liu, Liang wrote:
Thanks for the information. I installed the mpi version with "sudo
apt-get install gromacs-openmpi" under Ubuntu.
Then run "mdrun_mpi -s md.tpr -replex 10 -multi 10"? Another error
appears, "The number of nodes (1) is not a multiple of the number of
simulations (10)". Wha
Thanks for the information. I installed the mpi version with "sudo apt-get
install gromacs-openmpi" under Ubuntu.
Then run "mdrun_mpi -s md.tpr -replex 10 -multi 10"? Another error appears,
"The number of nodes (1) is not a multiple of the number of simulations
(10)". What is this for?
On Wed, S
Liu, Liang wrote:
Does that mean I have to use MPI? I got an error "mdrun -multi is not
supported with the thread library.Please compile GROMACS with MPI
support" after run "mdrun -s md.tpr -multi 10 -replex 10"
Per the error message, yes.
-Justin
On Wed, Sep 28, 2011 at 12:58 PM, Justin
Does that mean I have to use MPI? I got an error "mdrun -multi is not
supported with the thread library.Please compile GROMACS with MPI support"
after run "mdrun -s md.tpr -multi 10 -replex 10"
On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> Hi everyone,
>>
Liu, Liang wrote:
Hi everyone,
I tried to use Gromacs to run REMD simulation.
Firstly a set of (md#).mdp file are make and the grompp command can
generate the same amount of (md#).tpr file.
Assume # = 10,
then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10.
However, a fetal error s
Hi everyone,
I tried to use Gromacs to run REMD simulation.
Firstly a set of (md#).mdp file are make and the grompp command can generate
the same amount of (md#).tpr file.
Assume # = 10,
then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10.
However, a fetal error shows as "Need at least t
switched to a higher temperature.
Berk
> Date: Thu, 4 Dec 2008 03:19:17 +1100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] REMD problem in concept
>
> [EMAIL PROTECTED] wrote:
> > dG=dH-TdS
> >
> > so as T increases, so does t
[EMAIL PROTECTED] wrote:
dG=dH-TdS
so as T increases, so does the entropic contribution to the free energy
(=available energy). The potential energies stay the same when using a
temperature-independent forcefield (like all of the ones that come with
gromacs).
That's not quite right. The ave
dG=dH-TdS
so as T increases, so does the entropic contribution to the free
energy (=available energy). The potential energies stay the same when
using a temperature-independent forcefield (like all of the ones that
come with gromacs).
Your system will easily cross barriers on the order of
sarbani chattopadhyay wrote:
Hi,
Thank you for the reply. But in that case what helps the replica at
higher temperature cross the energy barrier? At higher temperature the
velocities will be higher.
For the same reason it can cross more easily at high T in non-REMD: when
there is more
Hi,
Thank you for the reply. But in that case what helps the replica at higher
temperature cross the energy barrier? At higher temperature the velocities will
be higher.
Thanks in advance,
Sarbani
On Tue, 02 Dec 2008 Mark Abraham wrote :
>sarbani chattopadhyay wrote:
>> Hi everybody,
sarbani chattopadhyay wrote:
Hi everybody,
I am having a doubt whether I have understood the
concepts of Replica
exchange molecular dynamics correctly or not.
When a pair of replicas are exchanged, the one at
higher temperature thet has
higher velo
Hi everybody,
I am having a doubt whether I have understood the
concepts of Replica
exchange molecular dynamics correctly or not.
When a pair of replicas are exchanged, the one at higher
temperature thet has
higher velocities, (which are rescaled a
31 matches
Mail list logo
