sir,
I have a basic doubt about remd simulation. In remd is it possible to
run 16 replicas in 8 processors?
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: pqah...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] REMD vs MD
Hi all,
I just want to ask you which is about REMD..I just understanding about
the MD simulation which is the basic one..If i have a several models
that i need to see the interaction between them is it okay to use
Hi all,
I just want to ask you which is about REMD..I just understanding about
the MD simulation which is the basic one..If i have a several models
that i need to see the interaction between them is it okay to use
MD?Or i need to use REMD instead?
Thanks in advance,
--
Best Regards,
Nur
Not sure what you're asking, but if you're providing twice as much
hardware, then invoke mpiexec_mpt suitably to tell it to use all of
that. Then, if you invoke mdrun_mpi the same way as you do now, it
will work out it can use twice as much hardware per replica.
Mark
On Mon, Aug 5, 2013 at 7:55
Sir
Yeah, I meant to use twice the hardware and i have already invoked
mpiexec_mpt.
the pbs script works fine if i start afresh mdrun of the tprs but if i
extend the simulation run by -cpi filename -noappend the run doesnt take
place.
On Mon, Aug 5, 2013 at 3:22 PM, Mark Abraham
On 8/5/13 6:36 AM, suhani nagpal wrote:
Sir
Yeah, I meant to use twice the hardware and i have already invoked
mpiexec_mpt.
the pbs script works fine if i start afresh mdrun of the tprs but if i
extend the simulation run by -cpi filename -noappend the run doesnt take
place.
AFAIK, you
Greetings
I'm running REMD of 96 replicas where the run.pbs is the following:
#!/bin/tcsh
#PBS -S /bin/tcsh
#PBS -l walltime=00:15:00
#PBS -q workq
#PBS -l select=8:ncpus=12:mpiprocs=12
#PBS -l place=scatter:excl
#PBS -V
# Go to the directory from which you submitted the job
cd $PBS_O_WORKDIR
Sir,
I did an 80 ns Remd simulation, after completion of the simulation
extended it up to 480 ns using tpbconv. Now the extended trajectories also
write on old trajectory files(traj.trr)?
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What does gmxcheck say about them?
On Aug 2, 2013 8:08 AM, Shine A shin...@iisertvm.ac.in wrote:
Sir,
I did an 80 ns Remd simulation, after completion of the simulation
extended it up to 480 ns using tpbconv. Now the extended trajectories also
write on old trajectory files(traj.trr)?
Hi!
On 2013-07-12 07:58, Shine A wrote:
Hi Sir,
Is it possible to run an REMD simulation having 16 replicas
in a
cluster(group of cpu) having 8 nodes. Here each node have 8
processors.
It is possible. If you have Gromacs (version = 4.6) compiled with MPI
and you specify the
Hi Sir,
Is it possible to run an REMD simulation having 16 replicas in a
cluster(group of cpu) having 8 nodes. Here each node have 8 processors.
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Sir,
I did an REMD for a peptide using implicit solvent model(8 replica 10 ns
each).The experimental structure of peptide in water look like
betasheet(from circular dichroism). But almost all conformations from
trajectory look like alpha-helices.Then how I can correlate experimental
and
On 7/8/13 11:13 AM, Shine A wrote:
Sir,
I did an REMD for a peptide using implicit solvent model(8 replica 10 ns
each).The experimental structure of peptide in water look like
betasheet(from circular dichroism). But almost all conformations from
trajectory look like alpha-helices.Then
Sir,
I did a 10 ns REMD simulation for a peptide, 8 replicas using amber
force field.Then extracted pdb file from the trajectory and clustered using
g_cluster. The I viewed the average structure of the cluster in pymol .But
here the atoms are merged togather.why it happends?Is there any
Not sure exactly what merging together means, for visualisation I
generally use vmd as this supports gromacs files directly.
Your problem might be to do with, using rlist, rcoulomb, and rvdw set to
0 is not the standard way to do an infinite cut-off normally you set
them to -1 as in the
On Tue, Jul 2, 2013 at 5:30 AM, Richard Broadbent
richard.broadben...@imperial.ac.uk wrote:
Not sure exactly what merging together means, for visualisation I
generally use vmd as this supports gromacs files directly.
If I understand correctly (and the OP can clarify if I haven't), it sounds
On 02/07/13 12:10, Justin Lemkul wrote:
On Tue, Jul 2, 2013 at 5:30 AM, Richard Broadbent
richard.broadben...@imperial.ac.uk wrote:
Not sure exactly what merging together means, for visualisation I
generally use vmd as this supports gromacs files directly.
If I understand correctly (and
Sir,
I trying to calculate ground state conformational ensemble of a
peptide by comparing experimental chemical shift and predicted chemical
shifts.For that I did REMD simulation at 8 temperatures.Then using
g_cluster clustered.Here is it reasonable to compare the chemical shift of
average
Justin answered this question about average structures earlier today.
Please read his answer.
Mark
On Tue, Jul 2, 2013 at 8:37 PM, Shine A shin...@iisertvm.ac.in wrote:
Sir,
I trying to calculate ground state conformational ensemble of a
peptide by comparing experimental chemical shift
Wrong way around. Decide what you want to observe and how you will
measure it *before* you do a simulation. Now you have a chance of
doing the right simulation.
On point, check out out chapter 8 of the manual.
Mark
On Thu, Jun 27, 2013 at 7:17 AM, Shine A shin...@iisertvm.ac.in wrote:
Hai Sir,
Hai Sir,
I did an REMD simulation for an intrinsically disordered
peptide.Then I extracted thousands of conformations(pdb) from trajectory.
Now I want to compare experimental Chemical Shifts and NOE distance for the
peptide with all these conformations.How can I do this?
--
gmx-users
Sir,
I did an remd simulation in implicit solvent for a peptide.I want to
compare the NOE distances from NMR and various conformations from REMD
output. Here how I get various conformations from remd trajectory? .Is any
script is available to find distance between two particular atoms?.How
There's number of analysis tools briefly described in chapter 8 of the
manual, and lots more detail in Appendix D. Have a look at what is
there, and do your background reading of the literature to see the
kinds of things people have done before you.
Mark
On Tue, Jun 25, 2013 at 1:18 PM, Shine A
On Tue, Jun 4, 2013 at 12:51 PM, suhani nagpal suhani.nag...@gmail.comwrote:
Hi all !
well, I'm working on REMD with 96 replicas, with temperature range 280K to
425.04K.
The NVT equilibration works well and graphs plotted show almost the
required temperature after equilibration.
Then,
Hi all !
well, I'm working on REMD with 96 replicas, with temperature range 280K to
425.04K.
The NVT equilibration works well and graphs plotted show almost the
required temperature after equilibration.
Then, after 3 ns of remd run , the edr - xvg files show initial
temperature atleast 40 -50
An acceptance ratio of 0.2/0.3 is normally best. The problem with high
acceptance ratio is that it means that a large portion of the exchanges are
just back and forth exchanges between consecutive exchange and are thus
disturbing the system more that actually helping sampling.
I do not know
Okay Sir, I will try two-three combinations this time and will report back
to you ...
On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote:
An acceptance ratio of 0.2/0.3 is normally best. The problem with high
acceptance ratio is that it means that a large portion of the
You have to convince yourself, not me :)) But I can give you my opinion …
On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote:
Okay Sir, I will try two-three combinations this time and will report back
to you ...
On Thu, May 16, 2013 at 5:25 PM, XAvier Periole
Dear Sir,
Here's the result of three different runs :
Temperature distribution for three trials
Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627
Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611
Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649
md.log
Indeed the Repeat-3 seems good. But I would guess you did not run too long,
right! That would explain the distribution of values!
On May 16, 2013, at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote:
Dear Sir,
Here's the result of three different runs :
Temperature distribution for
Okay, now I can start with large production runs .
On Thu, May 16, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote:
Indeed the Repeat-3 seems good. But I would guess you did not run too
long, right! That would explain the distribution of values!
On May 16, 2013, at 2:04 PM, bharat
On Thu, May 16, 2013 at 2:04 PM, bharat gupta bharat.85.m...@gmail.comwrote:
Dear Sir,
Here's the result of three different runs :
Temperature distribution for three trials
Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627
Repeat-2 280 299 319 340 363 388 414 441 471 503
Sorry to ask this simple question but how to read the replica_index and
replica_temp files. I tried to search a lot but didn't find any
information. As I have concatenated all log files and demuxed them. Here's
first 10 lines from both files:-
replica_index:
0 012345
They show which structure is in which ensemble, and the inverse. Look at
the exchange events reported in the .log files and work out which is which.
Mark
On Thu, May 16, 2013 at 5:25 PM, bharat gupta bharat.85.m...@gmail.comwrote:
Sorry to ask this simple question but how to read the
The plots that I showed in my last mail were for all replicas. I tried
plotting the first 500 ps of replica_index and replica_time files. I think
the plots look fine, and there could be problem with the plotting tool .
Here the link for both files ,
The interval between the exchange trial affect the efficiency of REMD but not
the the exchange ratio (at least in principle).
In you case I am not sure what the plot are showing! Are these showing all the
replicas? what are the units?
On May 14, 2013, at 5:07 AM, bharat gupta
Dear Sir,
I repeated the simulation again for 25 replicas with the following temp.
distribution .
280
289.1
298.5
308.2
318.2
328.6
339.3
350.3
361.7
373.5
385.6
398.1
411.1
424.4
438.3
452.5
467.2
482.4
498.1
514.3
531.0
548.3
566.1
584.5
603.5
623.2
The output of md.log file is :-
Replica
You need to increase the temperature gaps indeed if you want acceptance ratio
~0.2/0.3. But again this won't work with the water …
It is not clear what happens in your index file but probably a problem from
grace to plot so many points … you can try to increase the Max drawing path
length in
Dear Sir,
Here's the result for the REMD trial with large temperature gaps.
Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4
447.1 471.0 496.1 522.6 550.5 579.9 610.8
Out of md16.log :
Replica exchange statistics
Repl 249 attempts, 125 odd, 124 even
Repl average
Well, actually things do not look so good. But is it possible that grace is
actually no able to plot things correctly? You have line going throughout the
plot from complete-left to complete-right!
I am do not know what the t-rems calculator does but apparently it is not
optimal in your case.
Dear Sir,
Here's the temperature range that I got form t-remd :
1 300
2 323.7
3 348.75
4 375.23
5 403.22
6 432.83
7 464.14
8 497.24
9 532.26
10 569.32
11 608.51
according the above equation c should be somewhere around 2.37.
On Sat, May 11, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl
You are simulating in vacuo! Otherwise the temperature gaps are way too large …
If you want to analyse the sampling at 300 K, I would suggest you start you
first temperature lower, around 280/285 may be. At least to have your second
temperature at 300 K.
the value of c has absolutely not
Dear Sir,
I tried again with the following temp. ditribution, this time with 30
replicas (280 K -624K) and 500 ps simulation time for each one.
0 280
1 287.8
2 295.9
3 304.2
4 312.7
5 321.5
6 330.5
7 339.8
8 349.3
9 359.1
10 369.1
11 379.5
12 390.1
13 401.0
14 412.3
15 423.8
16 435.7
17 447.9
18
The values of exchange ratio look much better: they are similar over the range
of temperatures.
To reduce the ratio you have to increase the spacing between temperatures,
which means increase the value of c in the formula I gave earlier.
When you but the water in, the degrees of freedom
On Mon, May 6, 2013 at 3:48 AM, Kong xq xqkong...@gmail.com wrote:
Hi Mark,
Thanks for your great help. I am sorry for the negligence to state the
variation value correctly( it should be 0.011 rather than 0.11). Does this
somewhat small value indicate the generalized equilibrium achieved?
Dear GMX users,
I have some concerns about the statistics analysis of REMD which do
need your generous help.
I performed a 50ns isothermal-isobaric REMD simulation with 64 replicas
spaning from 300K to 390K. Then I want to do some statistics analysis for
the results. First, I calculated
On Sun, May 5, 2013 at 5:14 PM, Kong xq xqkong...@gmail.com wrote:
Dear GMX users,
I have some concerns about the statistics analysis of REMD which do
need your generous help.
I performed a 50ns isothermal-isobaric REMD simulation with 64 replicas
spaning from 300K to 390K. Then I
Hi Mark,
Thanks for your great help. I am sorry for the negligence to state the
variation value correctly( it should be 0.011 rather than 0.11). Does this
somewhat small value indicate the generalized equilibrium achieved? I will
search the papers you suggested. I am wondering whether the
Dear all,
We are stuck at the last stage of running a successful REMD.
We have obtained average potential energy by fitting the energy values from
initial MD.
We want to get the temperature spacing for 72 replicas, starting from 280K.
We have gone through numerous papers, but none of them explain
Dear
http://folding.bmc.uu.se/remd/ this may help you.
With best regards
On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com
wrote:
Dear all,
We are stuck at the last stage of running a successful REMD.
We have obtained average potential energy by fitting the
Thanks for that link.
I have used it, but it only takes system size properties. It doesn't take
the potential energy values at all.
I am looking if someone has used any alternate for temperature spacing
generation?
On Thu, Apr 4, 2013 at 1:16 PM, rama david ramadavidgr...@gmail.com wrote:
Dear
On Thu, Apr 4, 2013 at 10:17 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com
wrote:
Thanks for that link.
I have used it, but it only takes system size properties. It doesn't take
the potential energy values at all.
Actually it does, inasmuch as it uses parameters fitted to observed energy
Dear friends,
I am naive to the Replica exchange Molecular dynamics ( REMD).
I have plan to use REMD for temp. 310-320 K to my system.
I thoroughly search the Mailing-list Archive for the REMD problem.
It was a really helpful to start.
My system consist of peptide + water.
I used the
On 4/2/13 7:13 AM, rama david wrote:
Dear friends,
I am naive to the Replica exchange Molecular dynamics ( REMD).
I have plan to use REMD for temp. 310-320 K to my system.
I thoroughly search the Mailing-list Archive for the REMD problem.
It was a really helpful to start.
My
On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote:
On 4/2/13 7:13 AM, rama david wrote:
Dear friends,
I am naive to the Replica exchange Molecular dynamics ( REMD).
I have plan to use REMD for temp. 310-320 K to my system.
I thoroughly search the Mailing-list
I would look on some paper which temperature ranges and conditions
(NPT/NVT) were used for systems of a similar size and with a similar aim.
2013/4/2 rama david ramadavidgr...@gmail.com
Dear friends ,
Thank you justin and Mark for your suggestion
I increases my temp range from 310-360 K
Thank you Massimo sandal, Justin and mark ,
I also goes through the article and GMX archive.
But I confuse with the protocol ( I am naive in REMD .
So I want to conform protocol from the Expert and experience person )
I will be grateful to you for your suggestion.
On Tue, Apr 2, 2013 at
On 4/2/13 7:38 AM, Erik Marklund wrote:
On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote:
On 4/2/13 7:13 AM, rama david wrote:
Dear friends,
I am naive to the Replica exchange Molecular dynamics ( REMD).
I have plan to use REMD for temp. 310-320 K to my system.
I
On 4/2/13 9:24 AM, rama david wrote:
Thank you Massimo sandal, Justin and mark ,
I also goes through the article and GMX archive.
But I confuse with the protocol ( I am naive in REMD .
So I want to conform protocol from the Expert and experience person )
I will be grateful to you for your
Thank you justin.
I will do the same.
On Tue, Apr 2, 2013 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/2/13 9:24 AM, rama david wrote:
Thank you Massimo sandal, Justin and mark ,
I also goes through the article and GMX archive.
But I confuse with the protocol ( I am naive in
On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari
nixcrazyfor...@gmail.com wrote:
Dear all.
We are trying to run REMD on two proteins : 292 and 44 aa residues using
GROMACS 4.6.
We are unable to obtain the temperature spacing using REMD temperature
generator
I think determining k in the equation is not clear. How is it related to a
system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given starting
temperature, the temp. spacing will be the same. Is that correct?
On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
k is dimensionless. It does not relate to Boltzmann's constant. The
exponential spacing it produces would lead to replica exchange rates that
are constant over the T range, under certain assumptions (e.g. papers by
David A Kofke). In practice, it normally would not lead to such rates.
Whether
Sorry. I thought it was related to Boltzmann constt.
Then how is 'k' calculated ?
On Wed, Mar 13, 2013 at 8:17 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
k is dimensionless. It does not relate to Boltzmann's constant. The
exponential spacing it produces would lead to replica exchange
People often vary it to try to have an average exchange acceptance rate of
a level they think is useful. But that is only a proxy for what they really
want to achieve, which is replica flow, and it turns out that is a complex
thing and often requires a irregular spacing anyway.
Mark
On Wed, Mar
Hi all,
and thanks Mark, Chris and Xavier for your comments.
I finally managed to run the REMD simulation but i can not restart the
simulation or continue the simulation after it finished.
I tried with a test system and run two replicas for just 20 ps. After it
finished correctly i extended
That looks very strange. Please file an issue at
redmine.gromacs.orgincluding all your .tpr and .cpt, and assign it to
me.
Mark
On Thu, Dec 13, 2012 at 1:07 PM, Kenny Bravo Rodriguez
ke...@mpi-muelheim.mpg.de wrote:
Hi all,
and thanks Mark, Chris and Xavier for your comments.
I finally
Hi all,
I've read some earlier posts in the forum about replica exchange combined with
umbrella sampling but still not sure if the restrain potential defined in the
pull code will be included in the exchange criterion:
P(i-j) = min (1, exp[ (beta_i-beta_j)*(U(Ri, Dj) + U(Rj,Di) - U(Ri,Di) -
Hi all,
I've read some earlier posts in the forum about replica exchange combined
with umbrella sampling but still not sure if the restrain potential defined
in the pull code will be included in the exchange criterion:
P(i-j) = min (1, exp[ (beta_i-beta_j)*(U(Ri, Dj) + U(Rj,Di) - U(Ri,Di) -
Virtual sites also have a hidden benefit - not only can you take a longer
time step, but the width of the distribution of PE is relatively wider, so
you can have higher exchange probability for the same temperatures.
Mark
On Tue, Nov 20, 2012 at 12:34 AM, Christopher Neale
Dear All,
i am trying to performed REMD simulations using Gromacs.
My question is concerning the temperature distribution and the number of
replica.
I need to run 24 replicas of my system with a temperature range of
290-400 K. How can I select the temperatures values for each replica?
I tried
Well either you use more replicas or you reduce the temperature
range ...
There is no way around!
On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote:
Dear All,
i am trying to performed REMD simulations using Gromacs.
My question is concerning the temperature distribution and the
Xavier is right, except that you can also reduce the size of your system. You
can take larger steps in temperature
if you have fewer atoms. If you are using a cubic system, you can move to a
rhombic dodecahedron.
Even constraining all bonds will help a bit here (vs. harmonic bonds).
There
Dear Gromacs Users,
I would like to study structure of a positively charged protein in the
vicinity of DNA. To do this, I want to perform replica exchange molecular
dynamics simulations in which DNA is frozen and only the protein moves.
This way I can efficiently obtain the free energy landscape
On 11/9/12 9:02 AM, saber naderi wrote:
Dear Gromacs Users,
I would like to study structure of a positively charged protein in the
vicinity of DNA. To do this, I want to perform replica exchange molecular
dynamics simulations in which DNA is frozen and only the protein moves.
This way I can
I second everything that Justin Lemkul wrote. This recent paper (C. A.
Brackley, M. E. Cates, and D. Marenduzzo, Phys. Rev. Lett. 109:168103 (2012))
have a few weak points in my opinion, but demonstrate the artifacts that arise
from freezing the DNA.
Best,
Erik
9 nov 2012 kl. 20.42 skrev
hello:
I am trying to submit replica exchange jobs to cluster by following
command, but failed:
g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000
-reseed -1 -launch
Here is the log file:
---
Program g_tune_pme_d, VERSION
Hello,
Basically is telling you that the output (.tpr) file that grompp should
have created is not there to be read.
Check if grompp ran correctly and produced the wanted output. I suspect
that it may have failed for some reasons.
Hope this helps,
Cheers,
Davide
On 19/10/12 7:37 PM, Albert
hello David:
thanks for kind reply.
The .tpr file was created by grompp in cluster and there is no problem
for that.
thank you very much
Albert
On 10/19/2012 08:52 AM, Davide Mercadante wrote:
Hello,
Basically is telling you that the output (.tpr) file that grompp should
have created is
Hi Albert,
Please accept my apologies, I must have misread your e-mail. Effectively
everything seems to be right in the command line and I am not able to
understand either why you get the error.
Good luck.
Cheers,
Davide
On 19/10/12 7:54 PM, Albert mailmd2...@gmail.com wrote:
hello David:
On 10/19/12 2:37 AM, Albert wrote:
hello:
I am trying to submit replica exchange jobs to cluster by following command, but
failed:
g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1
-launch
Here is the log file:
Hi friends ,
I am new to the REMD simulation.
I read some thread from archive but they not clarify by queries that why I
am asking you on forum
I have following Queries:
1. I want to simulate protein by remd at physiological temp ( 310).
So my initial temp of replica
Hi Gromacs Users
I'm new to list, but hope to get a little help from someone experienced
with setting up some replica exhange simulations in explicit solvent. It
keeps exploding after app. 50 to 200 ps simulation time. It runs fine up
to there, and then suddently one or a couple of atoms
On 19/06/2012 5:55 PM, Esben Jannik Bjerrum wrote:
Hi Gromacs Users
I'm new to list, but hope to get a little help from someone experienced
with setting up some replica exhange simulations in explicit solvent. It
keeps exploding after app. 50 to 200 ps simulation time. It runs fine up
to
p.m.
Para: Discussion list for GROMACS users
Asunto: Re: [gmx-users] REMD question
Gromacs already supports replica exchange -- what particularly are you
implementing?
Equilibration of pressure is always a good idea -- even if you are running
NVT simulations, you want to get them
Dear Gromacs Users,
We are implementing REMD method in Gromacs in protein folding, in your web
page you give some steps that don´t mention any step about NPT
stabilization. This step is necessary to run REMD simulations?
Thank you in advance,
Nathalia
--
gmx-users mailing list
Gromacs already supports replica exchange -- what particularly are you
implementing?
Equilibration of pressure is always a good idea -- even if you are
running NVT simulations, you want to get them to be at the equilibrium
volume for your system and temperature choice, which will require
Hi,
I have notice that quite often people in REMD simulation use replicas in
lower than 300K temp.
Using for example temperature ranges from 250 to 450K
I am wondering what is the purpose of those replicas.
I have limited computational resources and I am wondering if for studing
175 aa protein is
On 27/04/2012 10:59 PM, Tomek Wlodarski wrote:
Hi,
I have notice that quite often people in REMD simulation use replicas
in lower than 300K temp.
Using for example temperature ranges from 250 to 450K
I am wondering what is the purpose of those replicas.
I have limited computational resources
Hi Mark,
Thanks for reply.
The problem is that I have never found in the papers reasoning behind the
the lower than 300K temperatures.
Moreover, authors were interested in properties in 300K or above.
I was wondering if this is not based on experience that REMD implemented in
gromacs works
If you are only interested in conformational sampling, then it makes
sense to start at 300 K or even higher - maybe 320 K. The main reason
for working at lower temperatures is if your system
is unstable - eg. if you expect that the molecule will be mostly
unfolded at 300 K and you want to
Dear gromacs users,
I have to perform REMD simulation, but since it is the first time I apply
this tecnique I have a question regarding system equilibration.
As far as I know, befaore starting the REMD each replica has to be
equlibrated. The equilibration has to be carried out in the NPT ensemble
On 03/23/2012 10:41 AM, francesco oteri wrote:
Dear gromacs users,
I have to perform REMD simulation, but since it is the first time I apply
this tecnique I have a question regarding system equilibration.
As far as I know, befaore starting the REMD each replica has to be
equlibrated. The
-users] REMD equilibration
Dear gromacs users,
I have to perform REMD simulation, but since it is the first time I apply this
tecnique I have a question regarding system equilibration.
As far as I know, befaore starting the REMD each replica has to be equlibrated.
The equilibration has to be carried
ensemble, in which you want to carry out the
production REMD.
Andreas
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of francesco oteri
Sent: 23 March 2012 09:41
To: Discussion list for GROMACS users
Subject: [gmx-users] REMD equilibration
Dear
francesco oteri wrote:
I understand,
I am planning to run REMD between 300 and 600 K, so I think it is better
equlibrating in NVT ensemble because at high temperature
water evaporates, is it?
Another very real concern is the stability of the simulations under NPT. At
higher
23 mar 2012 kl. 11.37 skrev Justin A. Lemkul:
francesco oteri wrote:
I understand,
I am planning to run REMD between 300 and 600 K, so I think it is better
equlibrating in NVT ensemble because at high temperature water evaporates,
is it?
Another very real concern is the stability
Hi,
I am trying to run a REMD of a peptide. But while executing the following
command after nvt and npt equilibration , I am getting the following error:-
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot
enable
On 12/01/2012 11:54 AM, bharat gupta wrote:
Hi,
I am trying to run a REMD of a peptide. But while executing the
following command after nvt and npt equilibration , I am getting the
following error:-
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared
On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:
Hi,
I am trying to run a REMD of a peptide. But while executing the
following command after nvt and npt equilibration , I am getting the
following error:-
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while
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