Greetings,
I would also be interested in an example of using REST via Hamiltonian REMD
in the current gromacs build. I'm particularly interested in enhanced
conformational sampling of 160-270 residue proteins. As it stands, I've
been unable to achieve any appreciable exchange probability in
Hi
Ive been looking for a sample input for a REST simulation but
so far have not been able to find one.
Does anybody have an example to share?
Ive seen the tutorial by Mark which mentions REST but I dont
see this included in the archived examples.
Am I missing something?
Thanks for any help
Hi, all-
Rest essentially scales the solute-solvent interactions, but maintains
the solute-solute interactions. This can be done solely with
Hamiltonian replica exchange, which is in 4.6. It's a bit tricky,
though. We plan on having something that does this automatically in
5.0 or 5.1, but it's
On Sat, Oct 26, 2013 at 06:06:59PM -0400, Michael Shirts wrote:
Hi, all-
Rest essentially scales the solute-solvent interactions, but maintains
the solute-solute interactions. This can be done solely with
Hamiltonian replica exchange, which is in 4.6. It's a bit tricky,
though. We plan on
Hi
I had tried using gromacs-4.6.1 to perform solute tempering. If you go
through terakawa's paper you have to describe the lambdas corresponding to
the temperatures. In your topology file define the params corresponding to
the two end states l=0 and l=1. Then define vdw, bonded and coulomb
Hi all,
I'm running a replica exchange simulation using gromacs 4.6.3 with the
command line:
mdrun_mpi -deffnm remd_ -multi 64 -replex 100 -nex 262144
I was expecting to get a log entry about the exchange every 100 steps but I
only got one every 1000 steps. I wonder if the output was suppressed
-replex 100 should emit to the log file every 100 steps. What was your
nstlog? Are you sure you are checking the right files? Can you
reproduce it?
Mark
On Tue, Jul 30, 2013 at 8:36 PM, Dejun Lin dejun@gmail.com wrote:
Hi all,
I'm running a replica exchange simulation using gromacs 4.6.3
Dear all
I would like running a replica exchange simulation using gromacs and gpu.
However when I Try to run the calculation I get this message
mdrun -multi is not supported with the thread library.
how do I compile gromacs ?
Could anyone confirm me the possibility to run 8 replicas on one GPUs
On Wed, Jul 17, 2013 at 4:09 PM, Jacopo Sgrignani sgri...@gmail.com wrote:
Dear all
I would like running a replica exchange simulation using gromacs and gpu.
However when I Try to run the calculation I get this message
mdrun -multi is not supported with the thread library.
REMD requires an
Thank you Mark and Francesco. I will be pleased to contribute with a fix in
case I come up with a fairly general solution for this issue.
Best regards,
João Henriques
On Thu, Apr 4, 2013 at 7:45 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Demux.pl pre-dates .cpt and -append. The only
Great.
Some of the data at the end of the .log file is easily recomputed from
the output at every exchange attempt once the .log files are
concatenated, but there will be loss of precision in re-computing the
average exchange acceptance probability, etc.
Mark
On Fri, Apr 5, 2013 at 10:37 AM,
So let me see if I understood what Francesco said correctly. Restarting a
REMD job after hitting the cluster wall-time limit resets the information
stored in the log files? Can someone shed some light on this subject?
Best regards,
João Henriques
--
gmx-users mailing listgmx-users@gromacs.org
This is what I meant,
in particular it is a problem when I want to analyze
the data regarding the exchange probability.
Francesco
2013/4/4 João Henriques joao.henriques.32...@gmail.com
So let me see if I understood what Francesco said correctly. Restarting a
REMD job after hitting the cluster
That's terrible! I was just about to restart 2 hefty REMD simulations...
Maybe I can move the original log files somewhere and combine them with the
restart ones afterwards by using a script. It's just an idea, because I
need to run Demux.pl on the final concatenated log file.
Any other issues I
if your -append option is activated (the default is yes),
maybe Demux.pl reads the exchanging from the .log taking into account the
time in the
log and so you don't need to do anything.
But I don't know how Demux.pl works :(
Francesco
2013/4/4 João Henriques joao.henriques.32...@gmail.com
Demux.pl pre-dates .cpt and -append. The only solution is to preserve your
.log files (e.g. with -noappend) and post-process. If you do that by
modifying demux.pl, please consider contributing your fix back.
Mark
On Apr 4, 2013 1:42 PM, francesco oteri francesco.ot...@gmail.com wrote:
if your
Dear gromacs users,
I ran a REMD on a HPC cluster equipped with a queue system.
For this reason I carried out the simulation dividing it in chuncks.
Because of this, each run started using the .cpt file from the previous one.
The simulation ran fine, but I noticed that the informations regarding
This is, unfortunately, normal. The REMD implementation was never updated
when the checkpointing mechanism was introduced, so this data is not
checkpointed.
Mark
On Sat, Mar 16, 2013 at 12:07 PM, francesco oteri francesco.ot...@gmail.com
wrote:
Dear gromacs users,
I ran a REMD on a HPC
On 20/07/2012 4:50 AM, leandro.bor...@usp.br wrote:
Dear users,
I'm currently doing some experiments with the implicit solvation
model running on GPUs with GROMACS.
I can make simple (conventional MD) simulations using the GPUs,
allowing great acceleration by using 1 GPU.
Dear users,
I'm currently doing some experiments with the implicit solvation
model running on GPUs with GROMACS.
I can make simple (conventional MD) simulations using the GPUs,
allowing great acceleration by using 1 GPU. However, I was wondering
about how to make Replica
Hi,
Occasionally I hear that one need to use WHAM( weighed histogram analysis)
method in collaboration with Temperature-Replica exchange simulation. But, I
was not understanding why one need to use WHAM with temperature-remd
simulation.
Can someone explain me ?
Does one need to use any
Dear gmx-users,
I am facing some problems while running replica exchange MD using Gromacs.
Few seconds after the job submission it ends with the following error message:
Initializing Replica Exchange
Repl There are 6 replicas:
Multi-checking the number of atoms ... OK
Multi-checking the
On 1/04/2011 6:03 PM, Ruchi Gupta wrote:
Dear gmx-users,
I am facing some problems while running replica exchange MD using Gromacs.
Few seconds after the job submission it ends with the following error message:
Initializing Replica Exchange
Repl There are 6 replicas:
Multi-checking the
On 01/04/2011, at 6:29 PM, Mark Abraham wrote:
On 1/04/2011 6:03 PM, Ruchi Gupta wrote:
Dear gmx-users,
I am facing some problems while running replica exchange MD using
Gromacs.
Few seconds after the job submission it ends with the following
error message:
Initializing Replica
On 1/04/2011 6:52 PM, bsmith wrote:
On 01/04/2011, at 6:29 PM, Mark Abraham wrote:
On 1/04/2011 6:03 PM, Ruchi Gupta wrote:
Dear gmx-users,
I am facing some problems while running replica exchange MD using
Gromacs.
Few seconds after the job submission it ends with the following
error
On 28/11/2010 4:49 AM, Sai Pooja wrote:
Hi,
I am running a script that uses mdrun of gromacs and does replica
exchange (not using -replex). The reason is that I want to use
different table files for different replicas. However, it seems that I
cannot supply unique table names. For example, if
Hi,
I am running a script that uses mdrun of gromacs and does replica exchange
(not using -replex). The reason is that I want to use different table files
for different replicas. However, it seems that I cannot supply unique table
names. For example, if I supply a table name different from
On 27/11/10 17:49, Sai Pooja wrote:
Hi,
I am running a script that uses mdrun of gromacs and does replica exchange
(not using -replex). The reason is that I want to use different table files
for different replicas. However, it seems that I cannot supply unique table
names. For example, if I
On 27/11/10 17:49, Sai Pooja wrote:
Hi,
I am running a script that uses mdrun of gromacs and does replica exchange
(not using -replex). The reason is that I want to use different table files
for different replicas. However, it seems that I cannot supply unique table
names. For example, if I
On 4/11/2010 1:53 AM, Sai Pooja wrote:
Hi,
I am running a the gromacs Replica exchange (NVT). However along with
the temperatures, I have also scaled a few paramters in the topology
file for each of the replicas for generating the .tpr files.
Everything seems to be running fine but is this a
Hi,
Does gromacs allow the use of a *different set* of energy tables for
different replicas? If not, any suggestions on how this can be done?
REM + 'different set of tables for each replica' + 'separate tables for
different pairs of energygroups'
Pooja
On Mon, Aug 30, 2010 at 7:25 PM, Mark
On 2010-09-01 17.32, Sai Pooja wrote:
Hi,
Does gromacs allow the use of a _different set_ of energy tables for
different replicas? If not, any suggestions on how this can be done?
REM + 'different set of tables for each replica' + 'separate tables for
different pairs of energygroups'
Pooja
Hello!
I'm doing a simple REMD test with 4 replicas.
Time step : 2 fs
Exchange : every 500fs
md_0.tpr md_1.tpr md_2.tpr md_3.tpr
mpiexec(or mpirun) -np 4 mdrun_mpi_d -deffnm md_ -multi 4 -replex 200
I got a error message.
##error##
100 steps, 2000.0 ps.
step 600 rank 3 in job 10
Hi,
This could be due to problems with MPICH.
Could you please try openmpi and report back?
Thanks,
Berk
From: sht_yc...@hotmail.com
To: gmx-users@gromacs.org
Date: Wed, 11 Aug 2010 18:09:00 +0900
Subject: [gmx-users] Replica Exchange problem in gmx-4.5 beta3
Hello!
I'm doing
, 2010 5:13
Subject: RE: [gmx-users] Replica Exchange MD on more than 64 processors
To: Discussion list for GROMACS users gmx-users@gromacs.org
---
|
Hi,
One issue could be MPI memory usage.
I have noticed that many MPI
Dear list
I recently came up with a problem concerning a replica exchange simulation. The
simulation is run
with gromacs-mpi in Version 4.0.7 compiled with following flags
--enable-threads --enable-mpi --with-fft=mkl -enable-double,
intel compiler version 11.0
mvapich version 1.1.0
mkl version
double precision,
which is almost never required. This will also make your simulations
a factor 1.4 faster.
Berk
Date: Tue, 2 Feb 2010 18:55:37 +0100
From: breue...@uni-koeln.de
To: gmx-users@gromacs.org
Subject: [gmx-users] Replica Exchange MD on more than 64 processors
Dear list
I
Dear list
I recently came up with a problem concerning a replica exchange simulation. The simulation is run
with gromacs-mpi in Version 4.0.7 compiled with following flags
--enable-threads --enable-mpi --with-fft=mkl -enable-double,
intel compiler version 11.0
mvapich version 1.1.0
mkl
On Mon, 28 Dec 2009, David van der Spoel wrote:
bharat v. adkar wrote:
On Mon, 28 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar
bharat v. adkar wrote:
On Mon, 28 Dec 2009, David van der Spoel wrote:
bharat v. adkar wrote:
On Mon, 28 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos -
REMD). I have to perform the REMD simulation with 35 different
temperatures.
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos -
REMD). I have to perform the REMD simulation with 35
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos -
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a
'protein in
water' system. I am following instructions
On Mon, 28 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a
bharat v. adkar wrote:
On Mon, 28 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos -
REMD). I have to perform the REMD simulation with 35 different
temperatures. As per advise on wiki, I equilibrated the system at
respective
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos -
REMD). I have to perform the REMD simulation with 35 different
temperatures. As per advise on wiki, I equilibrated the
It works just fine without RE.
On Sat, Apr 11, 2009 at 8:49 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
Joe Joe wrote:
Hi Justin,
Thanks for helping me with this.
On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Joe Joe wrote:
Joe Joe wrote:
It works just fine without RE.
OK well that sounds like after a replica exchange attempt, some data
structure isn't being (re-)constructed correctly. See if you can
construct a pair of .tpr files that reproduce the problem with replica
exchange after a small number of replica
Will do thanks.
Ilya
On Sun, Apr 12, 2009 at 7:50 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
Joe Joe wrote:
It works just fine without RE.
OK well that sounds like after a replica exchange attempt, some data
structure isn't being (re-)constructed correctly. See if you can construct a
Joe Joe wrote:
How do I determine what those values should be? How does it affect the
simulation?
The header of your log file should have printed what the initial guesses were.
The -dd option sets how many PP nodes there are in the domain decomposition;
using 4 cores, there are probably
Hi Justin,
Thanks for helping me with this.
On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Joe Joe wrote:
How do I determine what those values should be? How does it affect the
simulation?
The header of your log file should have printed what the initial guesses
On Sat, Apr 11, 2009 at 10:52 PM, Joe Joe ilcho...@gmail.com wrote:
Hi Justin,
Thanks for helping me with this.
On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Joe Joe wrote:
How do I determine what those values should be? How does it affect the
simulation?
Joe Joe wrote:
Hi Justin,
Thanks for helping me with this.
On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Joe Joe wrote:
How do I determine what those values should be? How does it
affect the simulation?
The
Joe Joe wrote:
Hi Justin,
Thanks for helping me with this.
On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Joe Joe wrote:
How do I determine what those values should be? How does it
affect the simulation?
The
Hi All,
I get the following error when running replica exchange. I have 32 replica's
with each replica running on 4 processors (128 total). How do I decrease the
domain decomposition cell size, -dss? What should I set it to?
Thanks,
Ilya
DD cell 2 0 0: Neighboring cells do not have atoms: 22217
Joe Joe wrote:
Hi All,
I get the following error when running replica exchange. I have 32
replica's with each replica running on 4 processors (128 total). How do
I decrease the domain decomposition cell size, -dss? What should I set
it to?
snip
You're getting some hints from mdrun, I'd
How do I determine what those values should be? How does it affect the
simulation?
thanks,
Ilya
On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Joe Joe wrote:
Hi All,
I get the following error when running replica exchange. I have 32
replica's with each replica
Hi everyone,
I will like to do Replica exchange simulation on a peptide.
We have a single
machine with 4 cpus and the gromacs3.3.2 is installed.
Thus I will be able to select only 4 temperature values. I came across the
T-REMD caculator
for temperature distributions .
sarbani chattopadhyay wrote:
Hi everyone,
I will like to do Replica exchange simulation on a
peptide. We have a single
machine with 4 cpus and the gromacs3.3.2 is installed.
Thus I will be able to select only 4 temperature values. I came across
the T-REMD caculator
for
Hi,
I do understand that reducing the number of replicas will limit my
temperature space,
but gromacs 3.3.2 can run 1 replica per node. Thus having 4 nodes , I can have
only 4
replicas. Thus in case I want to span a temperature space of 313K to 333K using
only 4
replicas, is there any
to
modify the setup of your MPI environment.
Berk
Date: Wed, 19 Nov 2008 10:17:52 +
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: Re: [gmx-users] Replica exchange temp. distribution
Hi,
I do understand that reducing the number of replicas will limit my
temperature space
sarbani chattopadhyay wrote:
Hi,
I do understand that reducing the number of replicas will limit my
temperature space,
but gromacs 3.3.2 can run 1 replica per node. Thus having 4 nodes , I
can have only 4
replicas. Thus in case I want to span a temperature space of 313K to
333K using
David Mobley wrote:
I have further replica exchange questions...
The order is that from low temperature to high temperature (as you could
check from the edr files) and when swaps happen the coordinates and
boxes are exchanged between CPUs.
OK. In other words the replicas are always ordered by
From: David Mobley [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] replica exchange output information
Date: Mon, 7 Jan 2008 10:40:44 -0800
David,
The order is that from
David van der Spoel wrote:
David Mobley wrote:
It would be nice to have this sort of information (i.e. that demux.pl
exists, and what it does) in the documentation or on the REMD page of
the wiki.
I've tried to write a bit about it:
http://wiki.gromacs.org/index.php/REMD#Post-processing
All,
Probably this should be obvious, but I've looked over the manual and
the wiki and the information is eluding me: When running replica
exchange in gromacs, are the output files written by replica number,
or by temperature number? That is, does ener0.edr, traj0.trr, etc.,
contain information
David Mobley wrote:
All,
Probably this should be obvious, but I've looked over the manual and
the wiki and the information is eluding me: When running replica
exchange in gromacs, are the output files written by replica number,
or by temperature number? That is, does ener0.edr, traj0.trr, etc.,
David Mobley wrote:
David,
The order is that from low temperature to high temperature (as you could
check from the edr files) and when swaps happen the coordinates and
boxes are exchanged between CPUs.
OK. In other words the replicas are always ordered by temperature.
Yes.
As a
David,
The order is that from low temperature to high temperature (as you could
check from the edr files) and when swaps happen the coordinates and
boxes are exchanged between CPUs.
OK. In other words the replicas are always ordered by temperature.
As a follow-up question, is there an
I have further replica exchange questions...
The order is that from low temperature to high temperature (as you could
check from the edr files) and when swaps happen the coordinates and
boxes are exchanged between CPUs.
OK. In other words the replicas are always ordered by temperature.
David Mobley wrote:
David,
The order is that from low temperature to high temperature (as you could
check from the edr files) and when swaps happen the coordinates and
boxes are exchanged between CPUs.
OK. In other words the replicas are always ordered by temperature.
As a follow-up
I am using 3.3.2 and 3.3.1 and I get the following problem with both of
them.
If I run replica exchange on 4 processors (2 and 4 are fine), the
simulations finish, but mpi gives the following errors, thus the job never
terminates
this is the end of my log file
Paul Whitford wrote:
I am using 3.3.2 and 3.3.1 and I get the following problem with both of
them.
If I run replica exchange on 4 processors (2 and 4 are fine), the
simulations finish, but mpi gives the following errors, thus the job
never terminates
this is the end of my log file
Thank you very much all for your consideration and fruitful advices.
Regards,
Monika
On Wed, 2007-12-05 at 18:15 +1100, Mark Abraham wrote:
Xavier Periole wrote:
Dear Monika,
the setup of a REMD simulation is actually quite straightforward.
In the following I describe steps that
Xavier Periole wrote:
Dear Monika,
the setup of a REMD simulation is actually quite straightforward.
In the following I describe steps that would lead you to have a
REMD simulation running on a given system. The success of the
simulation will depend entirely on the problem you are addressing
via REMD.This will be helpful.
Ozge.
-Original Message-
From: Monika Sharma [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Date: Fri, 30 Nov 2007 17:04:07 +0530 (IST)
Subject: [gmx-users] Replica Exchange MD using Gromacs
Dear All,
I am trying REMD for the first time using Gromacs
.
-Original Message-
From: Monika Sharma [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Date: Fri, 30 Nov 2007 17:04:07 +0530 (IST)
Subject: [gmx-users] Replica Exchange MD using Gromacs
Dear All,
I am trying REMD for the first time using Gromacs. But I am not finding
any much
PROTECTED]
To: gmx-users@gromacs.org
Date: Fri, 30 Nov 2007 17:04:07 +0530 (IST)
Subject: [gmx-users] Replica Exchange MD using Gromacs
Dear All,
I am trying REMD for the first time using Gromacs. But I am not finding
any much helpful material regarding the replica exchange using Gromacs.
Can anyone
Dear All,
I am trying REMD for the first time using Gromacs. But I am not finding
any much helpful material regarding the replica exchange using Gromacs.
Can anyone who has done REMD please let me know about any good tutorial
where I can understand the way this replica exchange work in gromacs
+0530 (IST)
Subject: [gmx-users] Replica Exchange MD using Gromacs
Dear All,
I am trying REMD for the first time using Gromacs. But I am not finding
any much helpful material regarding the replica exchange using Gromacs.
Can anyone who has done REMD please let me know about any good tutorial
where I
Hi,
After I was reading manual on REMD and mdrun, I understood that GROMACX
is capable to run REMD using just one node per replica (or single CPU
??). Is it right ?
Best
Arturas
___
gmx-users mailing listgmx-users@gromacs.org
The CVS version of Gromacs enables REMD simulations where each replica
can be run across multiple CPUs.
Bob
On 8/29/07, Arturas Ziemys [EMAIL PROTECTED] wrote:
Hi,
After I was reading manual on REMD and mdrun, I understood that GROMACX
is capable to run REMD using just one node per replica
How to access CVS of GROMACS ?
Robert Johnson wrote:
The CVS version of Gromacs enables REMD simulations where each replica
can be run across multiple CPUs.
Bob
On 8/29/07, Arturas Ziemys [EMAIL PROTECTED] wrote:
Hi,
After I was reading manual on REMD and mdrun, I understood that GROMACX
is
You can check out the Gromacs Wiki pages:
http://wiki.gromacs.org/index.php/Development
http://wiki.gromacs.org/index.php/CVS_HowTo
Bob
On 8/29/07, Arturas Ziemys [EMAIL PROTECTED] wrote:
How to access CVS of GROMACS ?
Robert Johnson wrote:
The CVS version of Gromacs enables REMD
Dear Sir,
i wanted to read the source code before doing REMD.
Thanks for your suggestions, i have found that already in the program and in
manual.
Reagrds
-
Once upon a time there was 1 GB storage in your inbox. Click here for happy
Dear all,
i want to start with the replica exchange method in gromacs, but i am not able
to search the script for that in the program.
Can anybody tell me by what name it is in the program and the location, as i
want to look into the program before starting.
Regards
Have a look at GMX/src/kernel/repl_ex.c
priya priya wrote:
Dear all,
i want to start with the replica exchange method in gromacs, but i am
not able to search the script for that in the program.
Can anybody tell me by what name it is in the program and the location,
as i want to look into the
priya priya wrote:
Dear all,
i want to start with the replica exchange method in gromacs, but i am
not able to search the script for that in the program.
Can anybody tell me by what name it is in the program and the location,
as i want to look into the program before starting.
Please
dear gromacs-users//
what would you think are good exchange rates between the replicas in a REMD?
something like this?
Replica exchange statistics
Repl 499 attempts, 250 odd, 249 even
Repl average probabilities:
Repl 0123456789 10 11 12
13 14
Carsten Baldauf wrote:
dear gromacs-users//
what would you think are good exchange rates between the replicas in a
REMD?
:-) I'm about to submit a paper partly on this topic... the short answer
is that most people publishing REMD exchange rates have one that is a
good deal lower. There's
://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Carsten Baldauf
Sent: Tuesday, July 10, 2007 5:43 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Replica Exchange MD ... Exchange rates
dear gromacs-users//
what
From: Mark Abraham [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] Replica Exchange MD ... Exchange rates
Date: Tue, 10 Jul 2007 20:15:31 +1000
Carsten Baldauf wrote
I'm getting an error message when feeding replica_index.xvg to trjcat.
Here is the command and the error message:
trjcat -f *.xtc -demux replica_index.xvg
Program trjcat, VERSION 3.3.99_development_20060330
Source code file: gmx_trjcat.c, line: 296
Fatal error:
Demuxing the same replica 1
Hello everyone,
I'm using the current development version of Gromacs to perform
replica exchange MD. Are there any Gromacs tools to aid in the
analysis of the trajectories. For example, are there tools that enable
trajectories grouped by temperature? Is there a way to determine the
temperature of
Robert Johnson wrote:
Hello everyone,
I'm using the current development version of Gromacs to perform
replica exchange MD. Are there any Gromacs tools to aid in the
analysis of the trajectories. For example, are there tools that enable
trajectories grouped by temperature? Is there a way to
Hi,
I do wonder whether replica exchange as implemented in Gromacs is
compatible with freezing part of a system. What I want to do is to
equilibrate a sub-part (18k atoms) of a large system (340k atoms)
by freezing the 322k surrounding atoms and doing replica exchange
on the small 18k atom
Hi all gmx-ers,
I have a doubt concerning the REMD setup. Let's say I want to use 12 cpus to
make a REMD at 2 different temp 300 and 400K of the same system.
Should I prepare every tpr file with the -np option set to 6?
and then run the mdrun with -np 12 -multi -s 300.tpr 400.tpr -replica
X
Thanks to all for the quick clarifications.
Andrea
- Original Message -
From: Xavier Periole [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, April 11, 2006 1:55 PM
Subject: Re: [gmx-users] replica exchange doubt
Andrea Carotti wrote:
Hi
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