RE: [gmx-users] REMD vs MD

[hanna pdb]

Hi, 
well I guess it depends on what models you mean...
REMD is a technique to enhance the conformational sampling. So if you have a 
e.g. a protein that is disordered or has large 
disordered parts. Using REMD several copies of the same system are simulated, 
each replica at a 
different temperature. Then, each replica can explore a different portion of 
the conformational space: the higher temperature replicas are able to move 
between different regions of the potential energy surface without staying in 
any of them, while the lowest temperature replicas can get trapped in local 
minima and are able to accurately explore the regions of the potential energy 
surface. This way you can obtain more information about conformational space 
then by simple MD.

This paper might help: Y. Sugita, Y. Okamoto, Chem. Phys. Let., 314, 261 (1999)

best

> Date: Thu, 5 Sep 2013 11:34:47 +0800
> From: 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
> MD?Or i need to use REMD instead?
> 
> Thanks in advance,
> 
> -- 
> Best Regards,
> 
> Nur Syafiqah Abdul Ghani,
> Theoretical and Computational Chemistry Laboratory,
> Department of Chemistry,
> Faculty of Science,
> Universiti Putra Malaysia,
> 43400 Serdang,
> Selangor.
> alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my
> -- 
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Re: [gmx-users] REMD run on higher nodes.

[Justin Lemkul]

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 can't change the number of processors mid-job and then try to use 
mdrun -cpi since information related to DD, etc is stored in the checkpoint 
files, which now do not match the previous run.


-Justin





On Mon, Aug 5, 2013 at 3:22 PM, Mark Abraham wrote:


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 AM, suhani nagpal 
wrote:

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
setenv MPI_GROUP_MAX 1024
setenv MPI_UNBUFFERED_STDIO 1

#mpiexec_mpt -np 24 ./exefile
mpiexec_mpt -np 96

/lustre/applications/GROMACS/gromacs-4.5.5/bin/mdrun_mpi

-s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend


So each replica runs at one processor.

Now, I want to run the remd at 16 nodes ( double ) so that each replica

is

subjected to 2 processors.


Kindly assist !

Thanks
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--
==

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Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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Re: [gmx-users] REMD run on higher nodes.

[suhani nagpal]

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 wrote:

> 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 AM, suhani nagpal 
> wrote:
> > 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
> > setenv MPI_GROUP_MAX 1024
> > setenv MPI_UNBUFFERED_STDIO 1
> >
> > #mpiexec_mpt -np 24 ./exefile
> > mpiexec_mpt -np 96
> /lustre/applications/GROMACS/gromacs-4.5.5/bin/mdrun_mpi
> > -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend
> >
> >
> > So each replica runs at one processor.
> >
> > Now, I want to run the remd at 16 nodes ( double ) so that each replica
> is
> > subjected to 2 processors.
> >
> >
> > Kindly assist !
> >
> > Thanks
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] REMD run on higher nodes.

[Mark Abraham]

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 AM, suhani nagpal  wrote:
> 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
> setenv MPI_GROUP_MAX 1024
> setenv MPI_UNBUFFERED_STDIO 1
>
> #mpiexec_mpt -np 24 ./exefile
> mpiexec_mpt -np 96 /lustre/applications/GROMACS/gromacs-4.5.5/bin/mdrun_mpi
> -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend
>
>
> So each replica runs at one processor.
>
> Now, I want to run the remd at 16 nodes ( double ) so that each replica is
> subjected to 2 processors.
>
>
> Kindly assist !
>
> Thanks
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] remd

[Mark Abraham]

What does gmxcheck say about them?
On Aug 2, 2013 8:08 AM, "Shine A"  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)?
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Re: [gmx-users] remd

[gigo]

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 number of replicas (-multi 16) in the mdrun command 
and 64 processors are allocated by mpirun, mdrun should start 4 MPI 
processes per each replica. It worked for me, at least. With OpenMP 
parallelization it would run faster, I have some problems with it 
though. Read the latest posts "Problems with REMD in Gromacs 4.6.3".

Best,
G
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Re: [gmx-users] remd

[Justin Lemkul]

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 how I can correlate experimental
and theoretical results.



Structural features are largely determined by the force field you've chosen to 
use.  Some have intrinsic biases that are usually well described in the literature.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] remd

[Mark Abraham]

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  wrote:
> 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 structure from a cluster to experimental chemical shift? But here
> the problem is atoms in the average structure look like overlapped to
> neighbor.why this?
> --
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Re: [gmx-users] remd

[Richard Broadbent]

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 the OP can clarify if I haven't), it sounds
like visualization of the average structure shows atoms overlapping one
another.  One should not necessarily expect anything reasonable from an
average structure.

http://www.gromacs.org/Documentation/Terminology/Average_Structure




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 manual.



I have never seen cutoffs set to -1. Is this a special trick in the code?
The OP's settings are correct for infinite cutoffs and use of all-vs-all
kernels.

Yes sorry that's my mistake I should never respond to the mailing list 
before having my morning coffee. Infinite cutoffs are specified with 
rlist=0 etc.


Sorry for the confusion.

Richard



Also the AMBER force field was parametrised with a cut-off it might,
depending on what you are trying to do, be advisable to use the cut-off
specified in the original papers and the wider literature for the AMBER
force field.



This is an important point, but finite cutoffs like those used in
explicit-solvent simulations (on the order of 1.0 nm) have, in my hands,
produced terrible results in an implicit environment (poor energy
conservation, loss of structure, etc).  Longer cutoffs are generally
recommended, and I only ever use infinite cutoffs in implicit systems.  It
is definitely worth some time doing validation of one's settings.



Richard


On 02/07/13 10:07, Shine A wrote:


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 problem
with my force field? My md.mdp file as follows.

RESHELIX ; -DFLEXIBLE -DPOSRES
   constraints =  none
   integrator  =  md
   dt  =  0.001   ; ps
   nsteps  =  1000 ; 1 ps = 10 ns
   nstcomm =  10
   nstcalcenergy   =  10
   nstxout =  500 ; frequency to write coordinates to
output
   trajectory
   nstvout =  0   ; frequency to write velocities to output
   trajectory; the last velocities are always written
   nstfout =  0   ; frequency to write forces to output
   trajectory
   nstlog  =  1000 ; frequency to write energies to log
   file
   nstenergy   =  1000 ; frequency to write energies to edr
file

   vdwtype =  cut-off
   coulombtype =  cut-off

   pbc =  no

   nstlist =  0
   ns_type =  simple
   rlist   =  0   ; this means all-vs-all (no cut-off),
which
   gets expensive for bigger systems
   rcoulomb=  0
   rvdw=  0

   comm-mode   =  angular
   comm-grps   =  system

   optimize_fft=  yes

   ; V-rescale temperature coupling is on
   Tcoupl  =  v-rescale
   tau_t   =  0.1
   tc_grps =  system
   ref_t   =  376.32
   ; Pressure coupling is off
   Pcoupl  =  no
   ; Generate velocites is on
   gen_vel =  yes
   gen_temp=  270




This doesn't make much sense to me.  If you're generating velocities, you
should be generating them for the target temperature.  If not, your
thermostat has to do some funny things to get it back on track.  With
V-rescale (or Berendsen, for that matter), you may not have an issue since
it relaxes quickly.  Other thermostats will cause you grief.

-Justin



   gen_seed=  -1


   ;
   ; Implicit solvent
   ;
   implicit_solvent=  GBSA
   gb_algorithm=  Still ; HCT ; OBC
   nstgbradii  =  1
   rgbradii=  0   ; [nm] Cut-off for the calculation of the
Born radii. Currently must be equal to rlist
   gb_epsilon_solvent  =  80; Dielectric constant for the implicit
solvent
   ; gb_saltconc   =  0 ; Salt concentration for implicit
solvent   models, currently not used
   sa_algorithm=  Ace-approximation
   sa_surface_tension  = -1

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Re: [gmx-users] remd

[Justin Lemkul]

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
like visualization of the average structure shows atoms overlapping one
another.  One should not necessarily expect anything reasonable from an
average structure.

http://www.gromacs.org/Documentation/Terminology/Average_Structure



> 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 manual.
>
>
I have never seen cutoffs set to -1. Is this a special trick in the code?
The OP's settings are correct for infinite cutoffs and use of all-vs-all
kernels.


> Also the AMBER force field was parametrised with a cut-off it might,
> depending on what you are trying to do, be advisable to use the cut-off
> specified in the original papers and the wider literature for the AMBER
> force field.
>
>
This is an important point, but finite cutoffs like those used in
explicit-solvent simulations (on the order of 1.0 nm) have, in my hands,
produced terrible results in an implicit environment (poor energy
conservation, loss of structure, etc).  Longer cutoffs are generally
recommended, and I only ever use infinite cutoffs in implicit systems.  It
is definitely worth some time doing validation of one's settings.


> Richard
>
>
> On 02/07/13 10:07, Shine A wrote:
>
>> 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 problem
>> with my force field? My md.mdp file as follows.
>>
>> RESHELIX ; -DFLEXIBLE -DPOSRES
>>   constraints =  none
>>   integrator  =  md
>>   dt  =  0.001   ; ps
>>   nsteps  =  1000 ; 1 ps = 10 ns
>>   nstcomm =  10
>>   nstcalcenergy   =  10
>>   nstxout =  500 ; frequency to write coordinates to
>> output
>>   trajectory
>>   nstvout =  0   ; frequency to write velocities to output
>>   trajectory; the last velocities are always written
>>   nstfout =  0   ; frequency to write forces to output
>>   trajectory
>>   nstlog  =  1000 ; frequency to write energies to log
>>   file
>>   nstenergy   =  1000 ; frequency to write energies to edr
>> file
>>
>>   vdwtype =  cut-off
>>   coulombtype =  cut-off
>>
>>   pbc =  no
>>
>>   nstlist =  0
>>   ns_type =  simple
>>   rlist   =  0   ; this means all-vs-all (no cut-off),
>> which
>>   gets expensive for bigger systems
>>   rcoulomb=  0
>>   rvdw=  0
>>
>>   comm-mode   =  angular
>>   comm-grps   =  system
>>
>>   optimize_fft=  yes
>>
>>   ; V-rescale temperature coupling is on
>>   Tcoupl  =  v-rescale
>>   tau_t   =  0.1
>>   tc_grps =  system
>>   ref_t   =  376.32
>>   ; Pressure coupling is off
>>   Pcoupl  =  no
>>   ; Generate velocites is on
>>   gen_vel =  yes
>>   gen_temp=  270
>>
>
This doesn't make much sense to me.  If you're generating velocities, you
should be generating them for the target temperature.  If not, your
thermostat has to do some funny things to get it back on track.  With
V-rescale (or Berendsen, for that matter), you may not have an issue since
it relaxes quickly.  Other thermostats will cause you grief.

-Justin


>   gen_seed=  -1
>>
>>   ;
>>   ; Implicit solvent
>>   ;
>>   implicit_solvent=  GBSA
>>   gb_algorithm=  Still ; HCT ; OBC
>>   nstgbradii  =  1
>>   rgbradii=  0   ; [nm] Cut-off for the calculation of the
>> Born radii. Currently must be equal to rlist
>>   gb_epsilon_solvent  =  80; Dielectric constant for the implicit
>> solvent
>>   ; gb_saltconc   =  0 ; Salt concentration for implicit
>> solvent   models, currently not used
>>   sa_algorithm=  Ace-approximation
>>   sa_surface_tension  = -1
>>
>>  --
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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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Re: [gmx-users] remd

[Richard Broadbent]

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 manual.


Also the AMBER force field was parametrised with a cut-off it might, 
depending on what you are trying to do, be advisable to use the cut-off 
specified in the original papers and the wider literature for the AMBER 
force field.


Richard

On 02/07/13 10:07, Shine A wrote:

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 problem
with my force field? My md.mdp file as follows.

RESHELIX ; -DFLEXIBLE -DPOSRES
  constraints =  none
  integrator  =  md
  dt  =  0.001   ; ps
  nsteps  =  1000 ; 1 ps = 10 ns
  nstcomm =  10
  nstcalcenergy   =  10
  nstxout =  500 ; frequency to write coordinates to output
  trajectory
  nstvout =  0   ; frequency to write velocities to output
  trajectory; the last velocities are always written
  nstfout =  0   ; frequency to write forces to output
  trajectory
  nstlog  =  1000 ; frequency to write energies to log
  file
  nstenergy   =  1000 ; frequency to write energies to edr file

  vdwtype =  cut-off
  coulombtype =  cut-off

  pbc =  no

  nstlist =  0
  ns_type =  simple
  rlist   =  0   ; this means all-vs-all (no cut-off), which
  gets expensive for bigger systems
  rcoulomb=  0
  rvdw=  0

  comm-mode   =  angular
  comm-grps   =  system

  optimize_fft=  yes

  ; V-rescale temperature coupling is on
  Tcoupl  =  v-rescale
  tau_t   =  0.1
  tc_grps =  system
  ref_t   =  376.32
  ; Pressure coupling is off
  Pcoupl  =  no
  ; Generate velocites is on
  gen_vel =  yes
  gen_temp=  270
  gen_seed=  -1

  ;
  ; Implicit solvent
  ;
  implicit_solvent=  GBSA
  gb_algorithm=  Still ; HCT ; OBC
  nstgbradii  =  1
  rgbradii=  0   ; [nm] Cut-off for the calculation of the
Born radii. Currently must be equal to rlist
  gb_epsilon_solvent  =  80; Dielectric constant for the implicit
solvent
  ; gb_saltconc   =  0 ; Salt concentration for implicit
solvent   models, currently not used
  sa_algorithm=  Ace-approximation
  sa_surface_tension  = -1


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Re: [gmx-users] REMD

[Mark Abraham]

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  wrote:
> 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?
> --
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Re: [gmx-users] remd analysis

[Mark Abraham]

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  wrote:
> 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 I
> get kinetics of folding from g_kinetics?
> --
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Re: [gmx-users] REMD run showing temperature range more than the equilibrated.

[Mark Abraham]

On Tue, Jun 4, 2013 at 12:51 PM, suhani nagpal wrote:

> 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 units up , and then gradually reduces to it's
> temperature.
>
> for example
> replica 0 has 280 temperature , for initial 40 ps, it shows temperature up
> till 335K an then, decline.
>

Sounds like you're re-generating velocities, or mismatching input files.


>
> and around 21st to 22nd replica, the exchange probability is varying a lot
> from 20% to 60%.
>
> so, my queries are
>
>  how to resolve this temperature issue and why is the exchange probability
> so abrupt at 21-22 replica ?
>

Can't say. Might even be real!

Mark
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Re: [gmx-users] REMD analysis

[bharat gupta]

Okay, now I can start with large production runs .


On Thu, May 16, 2013 at 11:10 PM, XAvier Periole  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 gupta 
> wrote:
>
> > 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 files output from three different trials:
> >
> > Repeat-1  .37  .28  .26  .30  .25  .29  .32  .35  .32  .35  .36  .32  .31
> > Repeat-2  .30  .33  .30  .25  .19  .27  .30  .31  .27  .40  .34  .31
> > Repeat-3  .18  .22  .26  .34  .26  .28  .25  .27  .27  .25  .27  .22
> >
> > I think as the required acceptance value all the three trials are fine,
> but
> > trail 3 would be much better to continue the further runs and anlysis ??
> >
> > So, is it fine to continue with the third simulation ?? But still the
> > problem is that I am not getting the exact graphs with xmgrace??
> >
> >
> > On Thu, May 16, 2013 at 5:36 PM, XAvier Periole 
> wrote:
> >
> >>
> >> You have to convince yourself, not me :)) But I can give you my opinion
> …
> >>
> >> On May 16, 2013, at 10:33 AM, bharat gupta 
> >> 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 
> >> 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
> 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 particularly the paper you mention but if you like what
> >> they
>  do, it is your choice at the end.
> 
>  Why don;t you just increase the spacing between the replicas? You will
>  need less replicas and potentially you could run two simulations
> >> instead of
>  one and evaluate the convergence ...
> 
>  On May 16, 2013, at 1:50 AM, bharat gupta 
>  wrote:
> 
> > 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 ,
> > https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp
> > https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp
> >
> > Now regarding the high acceptance ratio which is 0.5 , I came across
> a
> > paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they
> >> have
> > mentioned that their average acceptance ratio ranged between 30 to
> >> 80%. I
> > have a question here, how did they calculate the range for the
> average
> > acceptance ratio or is it average ratio for each replica . Actually,
> >> this
> > is the reference I am following. I am also interested in peptide
> >> folding
> > simulation, similar to this article.
> >
> > I want to know, whether the average acceptance ratio that I have got
> >> for
>  my
> > trial simulation is correct , together with the replica_temp and
> > replica_remd plots. Can I proceed for large production runs to
> complete
>  my
> > experiment ??
> >
> >
> >
> >
> > On Tue, May 14, 2013 at 6:34 PM, XAvier Periole 
>  wrote:
> >
> >>
> >> 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  >
> >> wrote:
> >>
> >>> 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 probabilities:
> >>> Repl 0123456789   10   11
> >> 12
> >>> 13   14   15
> >>> Repl  .40  .34  .38  .43  .43  .36  .45  .40  .37  .48  .47
>  .45
>  .47
> >>> .44  .46
> >>>
> >>> Repl  number of exchanges:
> >>> Repl 0123456789   10   11
> >> 12
> >>> 13   14   15
> 

Re: [gmx-users] REMD analysis

[XAvier Periole]

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  wrote:

> 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 files output from three different trials:
> 
> Repeat-1  .37  .28  .26  .30  .25  .29  .32  .35  .32  .35  .36  .32  .31
> Repeat-2  .30  .33  .30  .25  .19  .27  .30  .31  .27  .40  .34  .31
> Repeat-3  .18  .22  .26  .34  .26  .28  .25  .27  .27  .25  .27  .22
> 
> I think as the required acceptance value all the three trials are fine, but
> trail 3 would be much better to continue the further runs and anlysis ??
> 
> So, is it fine to continue with the third simulation ?? But still the
> problem is that I am not getting the exact graphs with xmgrace??
> 
> 
> On Thu, May 16, 2013 at 5:36 PM, XAvier Periole  wrote:
> 
>> 
>> You have to convince yourself, not me :)) But I can give you my opinion …
>> 
>> On May 16, 2013, at 10:33 AM, bharat gupta 
>> 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 
>> 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 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 particularly the paper you mention but if you like what
>> they
 do, it is your choice at the end.
 
 Why don;t you just increase the spacing between the replicas? You will
 need less replicas and potentially you could run two simulations
>> instead of
 one and evaluate the convergence ...
 
 On May 16, 2013, at 1:50 AM, bharat gupta 
 wrote:
 
> 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 ,
> https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp
> https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp
> 
> Now regarding the high acceptance ratio which is 0.5 , I came across a
> paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they
>> have
> mentioned that their average acceptance ratio ranged between 30 to
>> 80%. I
> have a question here, how did they calculate the range for the average
> acceptance ratio or is it average ratio for each replica . Actually,
>> this
> is the reference I am following. I am also interested in peptide
>> folding
> simulation, similar to this article.
> 
> I want to know, whether the average acceptance ratio that I have got
>> for
 my
> trial simulation is correct , together with the replica_temp and
> replica_remd plots. Can I proceed for large production runs to complete
 my
> experiment ??
> 
> 
> 
> 
> On Tue, May 14, 2013 at 6:34 PM, XAvier Periole 
 wrote:
> 
>> 
>> 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 
>> wrote:
>> 
>>> 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 probabilities:
>>> Repl 0123456789   10   11
>> 12
>>> 13   14   15
>>> Repl  .40  .34  .38  .43  .43  .36  .45  .40  .37  .48  .47  .45
 .47
>>> .44  .46
>>> 
>>> Repl  number of exchanges:
>>> Repl 0123456789   10   11
>> 12
>>> 13   14   15
>>> Repl   50   42   46   52   57   40   58   49   42   53   61   63
 56
>>> 57   58
>>> 
>>> Repl  average number of exchanges:
>>> Repl 0123456789   10   11
>> 12
>>> 13   14   15
>>> Repl  .40  .34  .37  .42  .46  .32  .46  .40  .34  .43  .49  .51
 .45
>>> .46  .46
>>> Average accep

Re: [gmx-users] REMD average acceptance ratio

[XAvier Periole]

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 (and thus the potential 
energy) will increase and the temperature distribution won't work at all! To 
cover the same temperature range you'll need much more temperatures. 

On May 11, 2013, at 19:59, bharat gupta  wrote:

> 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
> 18 460.4
> 19 473.3
> 20 486.6
> 21 500.2
> 22 514.3
> 23 528.7
> 24 543.5
> 25 558.7
> 26 574.4
> 27 590.4
> 28 607.0
> 29 624.0
> 
> 
> The output of   md29.log file is :-
> 
> Replica exchange statistics
> Repl  249 attempts, 125 odd, 124 even
> Repl  average probabilities:
> Repl 0123456789   10   11   12   13
>  14   15   16   17   18   19   20   21   22   23   24   25   26   27   28
>  29
> Repl  .68  .63  .62  .68  .71  .66  .69  .68  .71  .67  .64  .71  .69
> .71  .66  .69  .73  .73  .72  .73  .69  .71  .71  .74  .73  .70  .72  .74
> .71
> Repl  number of exchanges:
> Repl 0123456789   10   11   12   13
>  14   15   16   17   18   19   20   21   22   23   24   25   26   27   28
>  29
> Repl   81   77   79   90   93   78   91   80   88   78   81   92   96
> 94   81   83   90   92   83   97   89   87   91   94   88   84   85   89
> 86
> Repl  average number of exchanges:
> Repl 0123456789   10   11   12   13
>  14   15   16   17   18   19   20   21   22   23   24   25   26   27   28
>  29
> Repl  .65  .62  .63  .73  .74  .63  .73  .65  .70  .63  .65  .74  .77
> .76  .65  .67  .72  .74  .66  .78  .71  .70  .73  .76  .70  .68  .68  .72
> .69
> 
> 
> The average acceptance ration comes around 0.69 , which is very high. Now,
> in order to get the avg. acceptance ration between 0.2 to 0.3 and also all
> the replicas should exchange , what has to be done.
> 
> Here's the link for remd_index and remd_temp files
> https://www.dropbox.com/s/sgpblcdg9zh7f52/remd_temp.png
> https://www.dropbox.com/s/6hvqlqmu64mb2jy/remd_index.png
> 
> I want to that if I include water for the simulation, the same temp.
> distribution would work or not ??
> 
> 
> 
> 
> On Sun, May 12, 2013 at 12:10 AM, XAvier Periole  wrote:
> 
>> 
>> 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 importance … the temperature
>> distribution has … make some test to see how the acceptance ratio evolves …
>> 
>> On May 11, 2013, at 5:05 PM, bharat gupta 
>> wrote:
>> 
>>> 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 
>> wrote:
>>> 
 
 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. Did you try to use the simple rule Tn=T0 x exp(n
>> c),
 where T0 is close to your starting temperature and c is a constant that
>> you
 can tune and will define the spacing between the temperatures. From your
 current data you can guess the spacing and thus the c value you need.
>> Note
 that the exchange ratio is quickly converging in the simulation so you
>> can
 make a few trials …
 
 On May 11, 2013, at 1:40 PM, bharat gupta 
 wrote:
 
> Dear Sir,
> 
> Thank you for your reply. I choose the temperature distribution using
> t-remd calculator. Here's the link for index and temp files .
> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png
> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m.
> 
> 
> 
> 
> 
> 
> 
> On Sat, May 11, 2013 at 12:04 AM, XAvier Periole 
 wrote:
> 
>> 
>> The replicas seem indeed to have exchange. Using a colour for the #
>> replicas would help.
>> 
>> I could not access to the first link.
>> 

Re: [gmx-users] REMD average acceptance ratio

[bharat gupta]

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
18 460.4
19 473.3
20 486.6
21 500.2
22 514.3
23 528.7
24 543.5
25 558.7
26 574.4
27 590.4
28 607.0
29 624.0


The output of   md29.log file is :-

Replica exchange statistics
Repl  249 attempts, 125 odd, 124 even
Repl  average probabilities:
Repl 0123456789   10   11   12   13
  14   15   16   17   18   19   20   21   22   23   24   25   26   27   28
  29
Repl  .68  .63  .62  .68  .71  .66  .69  .68  .71  .67  .64  .71  .69
 .71  .66  .69  .73  .73  .72  .73  .69  .71  .71  .74  .73  .70  .72  .74
 .71
Repl  number of exchanges:
Repl 0123456789   10   11   12   13
  14   15   16   17   18   19   20   21   22   23   24   25   26   27   28
  29
Repl   81   77   79   90   93   78   91   80   88   78   81   92   96
94   81   83   90   92   83   97   89   87   91   94   88   84   85   89
86
Repl  average number of exchanges:
Repl 0123456789   10   11   12   13
  14   15   16   17   18   19   20   21   22   23   24   25   26   27   28
  29
Repl  .65  .62  .63  .73  .74  .63  .73  .65  .70  .63  .65  .74  .77
 .76  .65  .67  .72  .74  .66  .78  .71  .70  .73  .76  .70  .68  .68  .72
 .69


The average acceptance ration comes around 0.69 , which is very high. Now,
in order to get the avg. acceptance ration between 0.2 to 0.3 and also all
the replicas should exchange , what has to be done.

Here's the link for remd_index and remd_temp files
https://www.dropbox.com/s/sgpblcdg9zh7f52/remd_temp.png
https://www.dropbox.com/s/6hvqlqmu64mb2jy/remd_index.png

I want to that if I include water for the simulation, the same temp.
distribution would work or not ??




On Sun, May 12, 2013 at 12:10 AM, XAvier Periole  wrote:

>
> 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 importance … the temperature
> distribution has … make some test to see how the acceptance ratio evolves …
>
> On May 11, 2013, at 5:05 PM, bharat gupta 
> wrote:
>
> > 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 
> wrote:
> >
> >>
> >> 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. Did you try to use the simple rule Tn=T0 x exp(n
> c),
> >> where T0 is close to your starting temperature and c is a constant that
> you
> >> can tune and will define the spacing between the temperatures. From your
> >> current data you can guess the spacing and thus the c value you need.
> Note
> >> that the exchange ratio is quickly converging in the simulation so you
> can
> >> make a few trials …
> >>
> >> On May 11, 2013, at 1:40 PM, bharat gupta 
> >> wrote:
> >>
> >>> Dear Sir,
> >>>
> >>> Thank you for your reply. I choose the temperature distribution using
> >>> t-remd calculator. Here's the link for index and temp files .
> >>> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png
> >>> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Sat, May 11, 2013 at 12:04 AM, XAvier Periole 
> >> wrote:
> >>>
> 
>  The replicas seem indeed to have exchange. Using a colour for the #
>  replicas would help.
> 
>  I could not access to the first link.
> 
>  Note also that the increase of exchange ratio with the temperature
> >> suggest
>  the distribution of the temperature is not optimal and may be with
> >> regular
>  intervals? You want to use a exponential distribution.
> 
>  On May 10, 2013, at 4:53 PM, bharat gupta 
>  wrote:
> 
> > Dear gmx members,
> >
> > I have posted the same question previously , but I didn't get any
> >> reply.
> > So, if anyone can help me out ...
> >
> > I performed a REMD simulation on a peptide 384 atoms (24 residues).
> In
> > total 11 replicas were simulated for a period of 50ns each. The
> >> exchange
> > was allwoed at every 1000 steps. The output of md.log f

Re: [gmx-users] REMD average acceptance ratio

[XAvier Periole]

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 importance … the temperature distribution has 
… make some test to see how the acceptance ratio evolves … 

On May 11, 2013, at 5:05 PM, bharat gupta  wrote:

> 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  wrote:
> 
>> 
>> 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. Did you try to use the simple rule Tn=T0 x exp(n c),
>> where T0 is close to your starting temperature and c is a constant that you
>> can tune and will define the spacing between the temperatures. From your
>> current data you can guess the spacing and thus the c value you need. Note
>> that the exchange ratio is quickly converging in the simulation so you can
>> make a few trials …
>> 
>> On May 11, 2013, at 1:40 PM, bharat gupta 
>> wrote:
>> 
>>> Dear Sir,
>>> 
>>> Thank you for your reply. I choose the temperature distribution using
>>> t-remd calculator. Here's the link for index and temp files .
>>> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png
>>> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m.
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Sat, May 11, 2013 at 12:04 AM, XAvier Periole 
>> wrote:
>>> 
 
 The replicas seem indeed to have exchange. Using a colour for the #
 replicas would help.
 
 I could not access to the first link.
 
 Note also that the increase of exchange ratio with the temperature
>> suggest
 the distribution of the temperature is not optimal and may be with
>> regular
 intervals? You want to use a exponential distribution.
 
 On May 10, 2013, at 4:53 PM, bharat gupta 
 wrote:
 
> Dear gmx members,
> 
> I have posted the same question previously , but I didn't get any
>> reply.
> So, if anyone can help me out ...
> 
> I performed a REMD simulation on a peptide 384 atoms (24 residues). In
> total 11 replicas were simulated for a period of 50ns each. The
>> exchange
> was allwoed at every 1000 steps. The output of md.log file is :
> 
> Replica exchange statistics
> Repl  24999 attempts, 12500 odd, 12499 even
> Repl  average probabilities:
> Repl 0123456789   10
> Repl  .16  .16  .16  .17  .18  .21  .24  .26  .28  .30
> Repl  number of exchanges:
> Repl 0123456789   10
> Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703
> Repl  average number of exchanges:
> Repl 0123456789   10
> Repl  .16  .16  .17  .17  .17  .21  .24  .26  .28  .30
> 
> The acceptance ratio for each replica and average acceptance ratio is
>> as
> calculated below :-
> 
>  accp. ratio
> 2038 0.16304
> 2007 0.16056
> 2065 0.1652
> 2117 0.16936
> 2182 0.17456
> 2587 0.20696
> 3022 0.24176
> 3213 0.25704
> 3554 0.28432
> 3703 0.29624
> 0.211904 (avg accp ratio) (Is this value correct ??)
> 
> The Pdes used while generating temp. range was also 0.2. Does that mean
> that  replicas have exchanged for the given temp.range ??.  Here's the
 link
> for both remd_temp and remd_index files (
> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png<
 
>> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810
> )
> , (
> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m<
 
>> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m&cid=1368069857486-810
> 
> )
> 
> --
> Bharat
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
 --
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 http://lists.gromacs.org/mailman/listinfo/gmx-users
 * Please search the archive at
 http://www.gromacs.org/Supp

Re: [gmx-users] REMD average acceptance ratio

[bharat gupta]

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  wrote:

>
> 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. Did you try to use the simple rule Tn=T0 x exp(n c),
> where T0 is close to your starting temperature and c is a constant that you
> can tune and will define the spacing between the temperatures. From your
> current data you can guess the spacing and thus the c value you need. Note
> that the exchange ratio is quickly converging in the simulation so you can
> make a few trials …
>
> On May 11, 2013, at 1:40 PM, bharat gupta 
> wrote:
>
> > Dear Sir,
> >
> > Thank you for your reply. I choose the temperature distribution using
> > t-remd calculator. Here's the link for index and temp files .
> > https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png
> > https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m.
> >
> >
> >
> >
> >
> >
> >
> > On Sat, May 11, 2013 at 12:04 AM, XAvier Periole 
> wrote:
> >
> >>
> >> The replicas seem indeed to have exchange. Using a colour for the #
> >> replicas would help.
> >>
> >> I could not access to the first link.
> >>
> >> Note also that the increase of exchange ratio with the temperature
> suggest
> >> the distribution of the temperature is not optimal and may be with
> regular
> >> intervals? You want to use a exponential distribution.
> >>
> >> On May 10, 2013, at 4:53 PM, bharat gupta 
> >> wrote:
> >>
> >>> Dear gmx members,
> >>>
> >>> I have posted the same question previously , but I didn't get any
> reply.
> >>> So, if anyone can help me out ...
> >>>
> >>> I performed a REMD simulation on a peptide 384 atoms (24 residues). In
> >>> total 11 replicas were simulated for a period of 50ns each. The
> exchange
> >>> was allwoed at every 1000 steps. The output of md.log file is :
> >>>
> >>> Replica exchange statistics
> >>> Repl  24999 attempts, 12500 odd, 12499 even
> >>> Repl  average probabilities:
> >>> Repl 0123456789   10
> >>> Repl  .16  .16  .16  .17  .18  .21  .24  .26  .28  .30
> >>> Repl  number of exchanges:
> >>> Repl 0123456789   10
> >>> Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703
> >>> Repl  average number of exchanges:
> >>> Repl 0123456789   10
> >>> Repl  .16  .16  .17  .17  .17  .21  .24  .26  .28  .30
> >>>
> >>> The acceptance ratio for each replica and average acceptance ratio is
> as
> >>> calculated below :-
> >>>
> >>>   accp. ratio
> >>> 2038 0.16304
> >>> 2007 0.16056
> >>> 2065 0.1652
> >>> 2117 0.16936
> >>> 2182 0.17456
> >>> 2587 0.20696
> >>> 3022 0.24176
> >>> 3213 0.25704
> >>> 3554 0.28432
> >>> 3703 0.29624
> >>> 0.211904 (avg accp ratio) (Is this value correct ??)
> >>>
> >>> The Pdes used while generating temp. range was also 0.2. Does that mean
> >>> that  replicas have exchanged for the given temp.range ??.  Here's the
> >> link
> >>> for both remd_temp and remd_index files (
> >>> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png<
> >>
> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810
> >>> )
> >>> , (
> >>> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m<
> >>
> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m&cid=1368069857486-810
> >>>
> >>> )
> >>>
> >>> --
> >>> Bharat
> >>> --
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>> * Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-users-requ...@gromacs.org.
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> * Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >
> >
> >
> > --
> > Bharat
> > Ph.D. Candidate
> > Biomolecular Engineering Laboratory
> > Pusan National University
> > South Korea
> > Mobile no. - 010-5818-3680
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search

Re: [gmx-users] REMD average acceptance ratio

[XAvier Periole]

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. Did you try to use the simple rule Tn=T0 x exp(n c), 
where T0 is close to your starting temperature and c is a constant that you can 
tune and will define the spacing between the temperatures. From your current 
data you can guess the spacing and thus the c value you need. Note that the 
exchange ratio is quickly converging in the simulation so you can make a few 
trials … 

On May 11, 2013, at 1:40 PM, bharat gupta  wrote:

> Dear Sir,
> 
> Thank you for your reply. I choose the temperature distribution using
> t-remd calculator. Here's the link for index and temp files .
> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png
> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m.
> 
> 
> 
> 
> 
> 
> 
> On Sat, May 11, 2013 at 12:04 AM, XAvier Periole  wrote:
> 
>> 
>> The replicas seem indeed to have exchange. Using a colour for the #
>> replicas would help.
>> 
>> I could not access to the first link.
>> 
>> Note also that the increase of exchange ratio with the temperature suggest
>> the distribution of the temperature is not optimal and may be with regular
>> intervals? You want to use a exponential distribution.
>> 
>> On May 10, 2013, at 4:53 PM, bharat gupta 
>> wrote:
>> 
>>> Dear gmx members,
>>> 
>>> I have posted the same question previously , but I didn't get any reply.
>>> So, if anyone can help me out ...
>>> 
>>> I performed a REMD simulation on a peptide 384 atoms (24 residues). In
>>> total 11 replicas were simulated for a period of 50ns each. The exchange
>>> was allwoed at every 1000 steps. The output of md.log file is :
>>> 
>>> Replica exchange statistics
>>> Repl  24999 attempts, 12500 odd, 12499 even
>>> Repl  average probabilities:
>>> Repl 0123456789   10
>>> Repl  .16  .16  .16  .17  .18  .21  .24  .26  .28  .30
>>> Repl  number of exchanges:
>>> Repl 0123456789   10
>>> Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703
>>> Repl  average number of exchanges:
>>> Repl 0123456789   10
>>> Repl  .16  .16  .17  .17  .17  .21  .24  .26  .28  .30
>>> 
>>> The acceptance ratio for each replica and average acceptance ratio is as
>>> calculated below :-
>>> 
>>>   accp. ratio
>>> 2038 0.16304
>>> 2007 0.16056
>>> 2065 0.1652
>>> 2117 0.16936
>>> 2182 0.17456
>>> 2587 0.20696
>>> 3022 0.24176
>>> 3213 0.25704
>>> 3554 0.28432
>>> 3703 0.29624
>>> 0.211904 (avg accp ratio) (Is this value correct ??)
>>> 
>>> The Pdes used while generating temp. range was also 0.2. Does that mean
>>> that  replicas have exchanged for the given temp.range ??.  Here's the
>> link
>>> for both remd_temp and remd_index files (
>>> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png<
>> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810
>>> )
>>> , (
>>> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m<
>> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m&cid=1368069857486-810
>>> 
>>> )
>>> 
>>> --
>>> Bharat
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
> 
> 
> 
> -- 
> Bharat
> Ph.D. Candidate
> Biomolecular Engineering Laboratory
> Pusan National University
> South Korea
> Mobile no. - 010-5818-3680
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
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* Please don't post (un)subscrib

Re: [gmx-users] REMD Statistics

[Mark Abraham]

On Mon, May 6, 2013 at 3:48 AM, Kong xq  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?


It might be consistent with it, but it is never diagnostic of it. FWIW, I
have never seen an REMD study that attempted to address whether generalized
equilibrium was achieved.

I will
> search the papers you suggested. I am wondering whether the histogram is
> the gold standard for effectively constructing REMD flow. Moreover, how to
> do the potential energy overlap analysis in Gromacs, from the edr file for
> each replica ？Does any tool avalible in Gromacs to do this job ?
>

g_energy to get the data for each replica, then your favorite analysis
package to form histograms, and graphing program to overlay the plots. The
histograms can be done with g_analyze.

Mark
--
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Re: [gmx-users] REMD Statistics

[Kong xq]

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 histogram is
the gold standard for effectively constructing REMD flow. Moreover, how to
do the potential energy overlap analysis in Gromacs, from the edr file for
each replica ？Does any tool avalible in Gromacs to do this job ?

Xiangqian Kong

2013/5/6 Mark Abraham 

> On Sun, May 5, 2013 at 5:14 PM, Kong xq  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 want to do some statistics analysis for
> >>the results. First, I calculated the acceptance ratio for the adjacent
> >>pairs of temperatures (showing below). It seems that most of the values
> are
> >>uniform ( 0.25 +/- 0.11) .
>
>
> >That is an abnormally high variation in my experience. That could suggest
> >lack of generalized equilibrium on this time scale.
>
>
> >> Second, I  followed the track of replica 1 in
> >> the temperature space with the information from replica_temp.xvg
>  generated
> >> by demux.pl(demux.pl md0.log) scipt. However, the histogram（table
> below)
> >>indicated that the distribution of replica 1 in temperature space is not
> >> very uniform. So my question is why did the nonuniform temperature
> >> distribution of replica 1 occur given the fact that the acceptance ratio
> >> indicated a free random walk in temperature space ?
>
>
> The acceptance ratio is only a proxy for the existence of a random walk. It
> would be an amusing exercise to construct a toy system with replicas that
> would only exchange over a few adjacent temperatures. With suitable overlap
> of replicas constrained-temperature subranges, you could synthesise uniform
> exchange rates with no interesting replica flow. For example, if
> * state A is possible in the lower two-thirds of your temperature range,
> and
> * state B is possible in the upper two-thirds of your temperature range,
> and
> * no other states are possible, and
> * your initial configurations include examples of both A and B, and
> * A and B have no available interconversion pathways,
> then you can see apparently uniform neighbour exchange rates, and the REMD
> simulation is probably not being very useful in the normal case of trying
> to enhance statistics at the lowest temperature.
>
> The possibility of this kind of kinetic trapping is discussed in the REMD
> literature (including some rather old mentions). The extreme challenge of
> actually achieving replica flow efficiently is discussed in a series of
> papers from Nadler and Hansmann. Even spacing the temperatures for even
> replica flow for met-enkephalin is not trivial.
>
>


> What's more, whether a
> > longer simulation was needed to make a more flatter temperature
> > distribution for each replica?
> >
>
> Probably, but as above, not necessarily meaningful. It might be instructive
> to construct some random walks following the GROMACS REMD protocal with
> acceptance rate 0.25 and see whether your intuition is valid :-)
>
> By the way, I want to double check that each column except the first in
> > replica_temp.xvg represents a constant temperature corresponding to that
> > specified in tpr file, we may need to follow the replica index (such as 0
> > for the first replica) among different coloumns (or temperatures). Does
> > this make sense?
> >
>
> Look at the first row and column, and back at the .log files to see what
> exchanges take place. That's much better than trying a written description!
>
> Mark
>
>
> >
> >Best regards!
> >
> >Xiangqian Kong
> >
> > *The frequency of replica 1 in temperature space *
> >
> TemperatureFrequency31016.91%32011.58%33013.68%34013.79%35012.64%36011.60%
> > 3704.38%3805.26%39010.16%
> > --
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Re: [gmx-users] REMD Statistics

[Mark Abraham]

On Sun, May 5, 2013 at 5:14 PM, Kong xq  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 want to do some statistics analysis for
> the results. First, I calculated the acceptance ratio for the adjacent
> pairs of temperatures (showing below). It seems that most of the values are
> uniform ( 0.25 +/- 0.11) .


That is an abnormally high variation in my experience. That could suggest
lack of generalized equilibrium on this time scale.


> Second, I  followed the track of replica 1 in
> the temperature space with the information from replica_temp.xvg  generated
> by demux.pl(demux.pl md0.log) scipt. However, the histogram（table below)
> indicated that the distribution of replica 1 in temperature space is not
> very uniform. So my question is why did the nonuniform temperature
> distribution of replica 1 occur given the fact that the acceptance ratio
> indicated a free random walk in temperature space ?


The acceptance ratio is only a proxy for the existence of a random walk. It
would be an amusing exercise to construct a toy system with replicas that
would only exchange over a few adjacent temperatures. With suitable overlap
of replicas constrained-temperature subranges, you could synthesise uniform
exchange rates with no interesting replica flow. For example, if
* state A is possible in the lower two-thirds of your temperature range, and
* state B is possible in the upper two-thirds of your temperature range, and
* no other states are possible, and
* your initial configurations include examples of both A and B, and
* A and B have no available interconversion pathways,
then you can see apparently uniform neighbour exchange rates, and the REMD
simulation is probably not being very useful in the normal case of trying
to enhance statistics at the lowest temperature.

The possibility of this kind of kinetic trapping is discussed in the REMD
literature (including some rather old mentions). The extreme challenge of
actually achieving replica flow efficiently is discussed in a series of
papers from Nadler and Hansmann. Even spacing the temperatures for even
replica flow for met-enkephalin is not trivial.

What's more, whether a
> longer simulation was needed to make a more flatter temperature
> distribution for each replica?
>

Probably, but as above, not necessarily meaningful. It might be instructive
to construct some random walks following the GROMACS REMD protocal with
acceptance rate 0.25 and see whether your intuition is valid :-)

By the way, I want to double check that each column except the first in
> replica_temp.xvg represents a constant temperature corresponding to that
> specified in tpr file, we may need to follow the replica index (such as 0
> for the first replica) among different coloumns (or temperatures). Does
> this make sense?
>

Look at the first row and column, and back at the .log files to see what
exchanges take place. That's much better than trying a written description!

Mark


>
>Best regards!
>
>Xiangqian Kong
>
> *The frequency of replica 1 in temperature space *
> TemperatureFrequency31016.91%32011.58%33013.68%34013.79%35012.64%36011.60%
> 3704.38%3805.26%39010.16%
> --
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Re: [gmx-users] REMD temperature spacing formula

[Mark Abraham]

On Thu, Apr 4, 2013 at 10:17 AM, Nikunj Maheshwari  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
values, which you'd know from reading the abstract of the cited paper ;-).


> I am looking if someone has used any alternate for temperature spacing
> generation?
>

Not sure what you're asking for. But you could try the REMD how-to guide in
http://pubs.acs.org/doi/abs/10.1021/ct800016r, or the works of DA Kofke or UHE Hansmann will likely be instructive.

Mark

On Thu, Apr 4, 2013 at 1:16 PM, rama david  wrote:
>
> > 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 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 clearly
> > how
> > > they got the spacing values.
> > > Is there any equation/formula/web utility which gives the spacing?
> > >
> > > Any help will be highly appreciated.
> > >
> > > Thank you.
> > > Nikunj & Suhani
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] REMD temperature spacing formula

[Nikunj Maheshwari]

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  wrote:

> 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 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 clearly
> how
> > they got the spacing values.
> > Is there any equation/formula/web utility which gives the spacing?
> >
> > Any help will be highly appreciated.
> >
> > Thank you.
> > Nikunj & Suhani
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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Re: [gmx-users] REMD temperature spacing formula

[rama david]

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  wrote:

> 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 clearly how
> they got the spacing values.
> Is there any equation/formula/web utility which gives the spacing?
>
> Any help will be highly appreciated.
>
> Thank you.
> Nikunj & Suhani
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] REMD general protocol ...

[rama david]

Thank you justin.
I will do the same.



On Tue, Apr 2, 2013 at 10:06 PM, Justin Lemkul  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 REMD .
>> So I want to conform protocol from the Expert and experience person )
>>
>> I will be grateful to you  for your suggestion.
>>
>>
>>
> The best training experience would be to take a simple example from the
> literature and reproduce it.  It is very hard to try to teach someone
> completely via email, especially since we do not know the scope and goals
> of what you are doing.
>
> With respect to the question about pressure coupling stability over 310 -
> 360 K, I don't know offhand what to expect, but in general, I think this is
> a standard limitation within REMD and you'll probably encounter it.  Again,
> find a protocol for a similar system and try to get things working.  It
> will be easier to help you if you have a known objective that has been
> demonstrated to work.
>
> -Justin
>
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] REMD general protocol ...

[Justin Lemkul]

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 suggestion.




The best training experience would be to take a simple example from the 
literature and reproduce it.  It is very hard to try to teach someone completely 
via email, especially since we do not know the scope and goals of what you are 
doing.


With respect to the question about pressure coupling stability over 310 - 360 K, 
I don't know offhand what to expect, but in general, I think this is a standard 
limitation within REMD and you'll probably encounter it.  Again, find a protocol 
for a similar system and try to get things working.  It will be easier to help 
you if you have a known objective that has been demonstrated to work.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] REMD general protocol ...

[Justin Lemkul]

On 4/2/13 7:38 AM, Erik Marklund wrote:


On 2 Apr 2013, at 13:30, Justin Lemkul  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 Archive for the REMD problem.
It was a really helpful to start.

  My system consist of peptide + water.

I used the following work-flow, Would you please help me to find out
my mistakes...

1. energy minimesation for peptide  + solvent
2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file )
3. Make tpr file for each nvt run
4. Then separate  equilibration for each temp ( 4 equilibration steps  )
5. Then made NPT.mdp file for each temp ( 4 temp )
6. Then again equilibration for NPT at 4 temp.( 4 equilibration  steps )
7.   Then run md production  with -replex 1000  -multi 4  command ..

To determine the temp I used web-server  http://folding.bmc.uu.se/remd/

Please suggest me any improvements that are  possible to implement in
my work flow.



Such a narrow range of temperatures defeats the purpose of using REMD. 
Normally, a much larger range is used over many more simulations.  For 
near-ambient temperatures, NPT can be used, but if you include much higher 
temperatures, you should use NVT due to box instability upon exchanges.

-Justin


Sure, the enhanced sampling is basically gone, but you can deduce temperature 
dependences from such simulations and to some extent benefit from the mixing, 
can't you?



I suppose, but then why bother with the exchange overhead?  Seems to me that if 
you're only interested in temperature-dependent quantities, you can do that with 
independent simulations at different temperatures.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] REMD general protocol ...

[rama david]

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 6:45 PM, massimo sandal wrote:

> 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 
>
> > Dear friends ,
> > Thank you justin and Mark for your suggestion
> >
> > I increases my temp range from 310-360 K
> > Now I get 20 replicas .
> >
> > Is in such large temp range wlll it be good to use NPT.
> >
> > Would you tell me the temp differences in which box instability generally
> > arises ..
> >
> >
> >
> > Is my working-flow right or need to change much
> >
> >
> > Thank you
> > With Best Regards..
> >
> >
> >
> >
> > On Tue, Apr 2, 2013 at 5:08 PM, Erik Marklund 
> > wrote:
> >
> > >
> > > On 2 Apr 2013, at 13:30, Justin Lemkul  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 Archive for the REMD problem.
> > > >> It was a really helpful to start.
> > > >>
> > > >>  My system consist of peptide + water.
> > > >>
> > > >> I used the following work-flow, Would you please help me to find out
> > > >> my mistakes...
> > > >>
> > > >> 1. energy minimesation for peptide  + solvent
> > > >> 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file )
> > > >> 3. Make tpr file for each nvt run
> > > >> 4. Then separate  equilibration for each temp ( 4 equilibration
> steps
> >  )
> > > >> 5. Then made NPT.mdp file for each temp ( 4 temp )
> > > >> 6. Then again equilibration for NPT at 4 temp.( 4 equilibration
> >  steps )
> > > >> 7.   Then run md production  with -replex 1000  -multi 4  command ..
> > > >>
> > > >> To determine the temp I used web-server
> > http://folding.bmc.uu.se/remd/
> > > >>
> > > >> Please suggest me any improvements that are  possible to implement
> in
> > > >> my work flow.
> > > >>
> > > >
> > > > Such a narrow range of temperatures defeats the purpose of using
> REMD.
> > > Normally, a much larger range is used over many more simulations.  For
> > > near-ambient temperatures, NPT can be used, but if you include much
> > higher
> > > temperatures, you should use NVT due to box instability upon exchanges.
> > > >
> > > > -Justin
> > >
> > > Sure, the enhanced sampling is basically gone, but you can deduce
> > > temperature dependences from such simulations and to some extent
> benefit
> > > from the mixing, can't you?
> > >
> > > Erik
> > >
> > > >
> > > > --
> > > > 
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Research Scientist
> > > > Department of Biochemistry
> > > > Virginia Tech
> > > > Blacksburg, VA
> > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > >
> > > > 
> > > > --
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> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] REMD general protocol ...

[massimo sandal]

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 

> Dear friends ,
> Thank you justin and Mark for your suggestion
>
> I increases my temp range from 310-360 K
> Now I get 20 replicas .
>
> Is in such large temp range wlll it be good to use NPT.
>
> Would you tell me the temp differences in which box instability generally
> arises ..
>
>
>
> Is my working-flow right or need to change much
>
>
> Thank you
> With Best Regards..
>
>
>
>
> On Tue, Apr 2, 2013 at 5:08 PM, Erik Marklund 
> wrote:
>
> >
> > On 2 Apr 2013, at 13:30, Justin Lemkul  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 Archive for the REMD problem.
> > >> It was a really helpful to start.
> > >>
> > >>  My system consist of peptide + water.
> > >>
> > >> I used the following work-flow, Would you please help me to find out
> > >> my mistakes...
> > >>
> > >> 1. energy minimesation for peptide  + solvent
> > >> 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file )
> > >> 3. Make tpr file for each nvt run
> > >> 4. Then separate  equilibration for each temp ( 4 equilibration steps
>  )
> > >> 5. Then made NPT.mdp file for each temp ( 4 temp )
> > >> 6. Then again equilibration for NPT at 4 temp.( 4 equilibration
>  steps )
> > >> 7.   Then run md production  with -replex 1000  -multi 4  command ..
> > >>
> > >> To determine the temp I used web-server
> http://folding.bmc.uu.se/remd/
> > >>
> > >> Please suggest me any improvements that are  possible to implement in
> > >> my work flow.
> > >>
> > >
> > > Such a narrow range of temperatures defeats the purpose of using REMD.
> > Normally, a much larger range is used over many more simulations.  For
> > near-ambient temperatures, NPT can be used, but if you include much
> higher
> > temperatures, you should use NVT due to box instability upon exchanges.
> > >
> > > -Justin
> >
> > Sure, the enhanced sampling is basically gone, but you can deduce
> > temperature dependences from such simulations and to some extent benefit
> > from the mixing, can't you?
> >
> > Erik
> >
> > >
> > > --
> > > 
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Research Scientist
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > 
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-requ...@gromacs.org.
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> >
> > --
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> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] REMD general protocol ...

[rama david]

Dear friends ,
Thank you justin and Mark for your suggestion

I increases my temp range from 310-360 K
Now I get 20 replicas .

Is in such large temp range wlll it be good to use NPT.

Would you tell me the temp differences in which box instability generally
arises ..



Is my working-flow right or need to change much


Thank you
With Best Regards..




On Tue, Apr 2, 2013 at 5:08 PM, Erik Marklund  wrote:

>
> On 2 Apr 2013, at 13:30, Justin Lemkul  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 Archive for the REMD problem.
> >> It was a really helpful to start.
> >>
> >>  My system consist of peptide + water.
> >>
> >> I used the following work-flow, Would you please help me to find out
> >> my mistakes...
> >>
> >> 1. energy minimesation for peptide  + solvent
> >> 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file )
> >> 3. Make tpr file for each nvt run
> >> 4. Then separate  equilibration for each temp ( 4 equilibration steps  )
> >> 5. Then made NPT.mdp file for each temp ( 4 temp )
> >> 6. Then again equilibration for NPT at 4 temp.( 4 equilibration  steps )
> >> 7.   Then run md production  with -replex 1000  -multi 4  command ..
> >>
> >> To determine the temp I used web-server  http://folding.bmc.uu.se/remd/
> >>
> >> Please suggest me any improvements that are  possible to implement in
> >> my work flow.
> >>
> >
> > Such a narrow range of temperatures defeats the purpose of using REMD.
> Normally, a much larger range is used over many more simulations.  For
> near-ambient temperatures, NPT can be used, but if you include much higher
> temperatures, you should use NVT due to box instability upon exchanges.
> >
> > -Justin
>
> Sure, the enhanced sampling is basically gone, but you can deduce
> temperature dependences from such simulations and to some extent benefit
> from the mixing, can't you?
>
> Erik
>
> >
> > --
> > 
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] REMD general protocol ...

[Erik Marklund]

On 2 Apr 2013, at 13:30, Justin Lemkul  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 Archive for the REMD problem.
>> It was a really helpful to start.
>> 
>>  My system consist of peptide + water.
>> 
>> I used the following work-flow, Would you please help me to find out
>> my mistakes...
>> 
>> 1. energy minimesation for peptide  + solvent
>> 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file )
>> 3. Make tpr file for each nvt run
>> 4. Then separate  equilibration for each temp ( 4 equilibration steps  )
>> 5. Then made NPT.mdp file for each temp ( 4 temp )
>> 6. Then again equilibration for NPT at 4 temp.( 4 equilibration  steps )
>> 7.   Then run md production  with -replex 1000  -multi 4  command ..
>> 
>> To determine the temp I used web-server  http://folding.bmc.uu.se/remd/
>> 
>> Please suggest me any improvements that are  possible to implement in
>> my work flow.
>> 
> 
> Such a narrow range of temperatures defeats the purpose of using REMD. 
> Normally, a much larger range is used over many more simulations.  For 
> near-ambient temperatures, NPT can be used, but if you include much higher 
> temperatures, you should use NVT due to box instability upon exchanges.
> 
> -Justin

Sure, the enhanced sampling is basically gone, but you can deduce temperature 
dependences from such simulations and to some extent benefit from the mixing, 
can't you?

Erik

> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] REMD general protocol ...

[Justin Lemkul]

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 system consist of peptide + water.

I used the following work-flow, Would you please help me to find out
my mistakes...

1. energy minimesation for peptide  + solvent
2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file )
3. Make tpr file for each nvt run
4. Then separate  equilibration for each temp ( 4 equilibration steps  )
5. Then made NPT.mdp file for each temp ( 4 temp )
6. Then again equilibration for NPT at 4 temp.( 4 equilibration  steps )
7.   Then run md production  with -replex 1000  -multi 4  command ..

To determine the temp I used web-server  http://folding.bmc.uu.se/remd/

Please suggest me any improvements that are  possible to implement in
my work flow.



Such a narrow range of temperatures defeats the purpose of using REMD. 
Normally, a much larger range is used over many more simulations.  For 
near-ambient temperatures, NPT can be used, but if you include much higher 
temperatures, you should use NVT due to box instability upon exchanges.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] REMD temperature spacing error

[Mark Abraham]

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 13, 2013 at 6:02 PM, Nikunj Maheshwari  wrote:

> 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  >wrote:
>
> > 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 constant exchange rate is even useful/meaningful is another
> matter
> > (e.g. papers by Walter Nadler & Ulrich Hansmann).
> >
> > Mark
> >
> > On Wed, Mar 13, 2013 at 12:49 PM, Nikunj Maheshwari <
> > nixcrazyfor...@gmail.com> wrote:
> >
> > > 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.com
> > > >wrote:
> > >
> > > > 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 (http://folding.bmc.uu.se/remd/) as it is giving myriad
> > > > > temperature ranges (in the order of 150 for 250-550K range)
> > > > >
> > > >
> > > > Sounds normal for the kind of system you seem to have. Higher numbers
> > of
> > > > degrees of freedom require closer temperature spacing.
> > > >
> > > > Is there any other way to determine the spacing? Can the equation
> > > > > T(i)=T(0).e(k.i) be used, as we are unable to comprehend it?
> > > > >
> > > >
> > > > Yes, but if you want exchanges to occur, there are constraints on the
> > > size
> > > > of k. What's so hard about T(i+1)=T(i)*k?
> > > >
> > > > Mark
> > > > --
> > > > gmx-users mailing listgmx-users@gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > > * Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-requ...@gromacs.org.
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> > > >
> > > --
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> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] REMD temperature spacing error

[Nikunj Maheshwari]

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 wrote:

> 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 constant exchange rate is even useful/meaningful is another matter
> (e.g. papers by Walter Nadler & Ulrich Hansmann).
>
> Mark
>
> On Wed, Mar 13, 2013 at 12:49 PM, Nikunj Maheshwari <
> nixcrazyfor...@gmail.com> wrote:
>
> > 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  > >wrote:
> >
> > > 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 (http://folding.bmc.uu.se/remd/) as it is giving myriad
> > > > temperature ranges (in the order of 150 for 250-550K range)
> > > >
> > >
> > > Sounds normal for the kind of system you seem to have. Higher numbers
> of
> > > degrees of freedom require closer temperature spacing.
> > >
> > > Is there any other way to determine the spacing? Can the equation
> > > > T(i)=T(0).e(k.i) be used, as we are unable to comprehend it?
> > > >
> > >
> > > Yes, but if you want exchanges to occur, there are constraints on the
> > size
> > > of k. What's so hard about T(i+1)=T(i)*k?
> > >
> > > Mark
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > > www interface or send it to gmx-users-requ...@gromacs.org.
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> > >
> > --
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> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] REMD temperature spacing error

[Mark Abraham]

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 constant exchange rate is even useful/meaningful is another matter
(e.g. papers by Walter Nadler & Ulrich Hansmann).

Mark

On Wed, Mar 13, 2013 at 12:49 PM, Nikunj Maheshwari <
nixcrazyfor...@gmail.com> wrote:

> 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  >wrote:
>
> > 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 (http://folding.bmc.uu.se/remd/) as it is giving myriad
> > > temperature ranges (in the order of 150 for 250-550K range)
> > >
> >
> > Sounds normal for the kind of system you seem to have. Higher numbers of
> > degrees of freedom require closer temperature spacing.
> >
> > Is there any other way to determine the spacing? Can the equation
> > > T(i)=T(0).e(k.i) be used, as we are unable to comprehend it?
> > >
> >
> > Yes, but if you want exchanges to occur, there are constraints on the
> size
> > of k. What's so hard about T(i+1)=T(i)*k?
> >
> > Mark
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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Re: [gmx-users] REMD temperature spacing error

[Nikunj Maheshwari]

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 wrote:

> 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 (http://folding.bmc.uu.se/remd/) as it is giving myriad
> > temperature ranges (in the order of 150 for 250-550K range)
> >
>
> Sounds normal for the kind of system you seem to have. Higher numbers of
> degrees of freedom require closer temperature spacing.
>
> Is there any other way to determine the spacing? Can the equation
> > T(i)=T(0).e(k.i) be used, as we are unable to comprehend it?
> >
>
> Yes, but if you want exchanges to occur, there are constraints on the size
> of k. What's so hard about T(i+1)=T(i)*k?
>
> Mark
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Re: [gmx-users] REMD temperature spacing error

[Mark Abraham]

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 (http://folding.bmc.uu.se/remd/) as it is giving myriad
> temperature ranges (in the order of 150 for 250-550K range)
>

Sounds normal for the kind of system you seem to have. Higher numbers of
degrees of freedom require closer temperature spacing.

Is there any other way to determine the spacing? Can the equation
> T(i)=T(0).e(k.i) be used, as we are unable to comprehend it?
>

Yes, but if you want exchanges to occur, there are constraints on the size
of k. What's so hard about T(i+1)=T(i)*k?

Mark
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Re: [gmx-users] REMD simulation

[Mark Abraham]

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 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 the time in each .tpr file
> and tried to continue the REMD simulation using the checkpoint files but i
> always get the same error message
>
> Multi-checking simulation part ... OK
> Multi-checking simulation part ... OK
> Reading file test0.tpr, VERSION 4.5.5 (single precision)
> Reading file test1.tpr, VERSION 4.5.5 (single precision)
> Multi-checking simulation part ... Multi-checking simulation part ...
> Multi-checking simulation part ... Multi-checking simulation part ...
> Multi-checking simulation part ... Multi-checking simulation part ...
> ERROR: 0031-250  task 6: Segmentation fault
> ERROR: 0031-250  task 7: Segmentation fault
> ERROR: 0031-250  task 2: Segmentation fault
> ERROR: 0031-250  task 1: Segmentation fault
> ERROR: 0031-250  task 5: Segmentation fault
> ERROR: 0031-250  task 3: Segmentation fault
> ERROR: 0031-250  task 0: Terminated
> ERROR: 0031-250  task 4: Terminated
>
> I used Gromacs 4.5.5 and the following commands:
>
> to start the REMD simulation:
> mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500
>
> to extend the time of the simulation in the .tpr files:
> tpbconv_d -s test_#.tpr -extend 20 -o test_#.tpr
>
> to continue the REMD simualtion:
> mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500
>
> Do i need to use any specific option to be able to continue the REMD
> simulation?
>
> Thanks in advanced
> Kenny
>
>
>
>
>
>
>   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<
>>  chris.ne...@mail.utoronto.ca>  wrote:
>>
>>  >  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 are lots of papers on this topic.
>>  >
>>  >  To see why you don't get any exchanges, construct histograms of your
>>  >  potential energies and you will see
>>  >  that they don't overlap. Also, it is inefficient to take evenly spaced
>>  >  temperatures. This is not your major problem,
>>  >  but read a bit on exponentially spaced temperatures for REMD.
>>  >
>>  >  Chris.
>>  >
>>  >  -- original message --
>>  >
>>  >  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
>>  >  >  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 the 
>> serverhttp://folding.bmc.uu.**se/remd/index.php
>>  but for
>>  >  >  my system it gives 50 replicas. If i try to take 24 evenly spaced
>>  >  >  values from the obtained list of temperature then
>>  >  >  the replicas do not exchange at all.
>>  >  >  I am using Gromacs 4.5.5 and my system has 6862 water molecules and
>>  >  >  535 atoms for the solute.
>>  >  >
>>  >  >  Thanks in advanced
>>  >  >  Kenny
>>  >  >
>>  >  --
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>>  >  
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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Re: [gmx-users] REMD simulation

[Mark Abraham]

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 <
chris.ne...@mail.utoronto.ca> wrote:

> 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 are lots of papers on this topic.
>
> To see why you don't get any exchanges, construct histograms of your
> potential energies and you will see
> that they don't overlap. Also, it is inefficient to take evenly spaced
> temperatures. This is not your major problem,
> but read a bit on exponentially spaced temperatures for REMD.
>
> Chris.
>
> -- original message --
>
> 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
> > 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 the server http://folding.bmc.uu.se/remd/index.php but for
> > my system it gives 50 replicas. If i try to take 24 evenly spaced
> > values from the obtained list of temperature then
> > the replicas do not exchange at all.
> > I am using Gromacs 4.5.5 and my system has 6862 water molecules and
> > 535 atoms for the solute.
> >
> > Thanks in advanced
> > Kenny
> >
> --
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Re: [gmx-users] REMD simulation

[XAvier Periole]

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  
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 the server http://folding.bmc.uu.se/remd/index.php but for  
my system it gives 50 replicas. If i try to take 24 evenly spaced  
values from the obtained list of temperature then

the replicas do not exchange at all.
I am using Gromacs 4.5.5 and my system has 6862 water molecules and  
535 atoms for the solute.


Thanks in advanced
Kenny

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Re: [gmx-users] REMD with Frozen DNA and Moving Protein

[Erik Marklund]

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 Justin Lemkul:

> 
> 
> 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 efficiently obtain the free energy landscape of the protein
>> close to [frozen] DNA.
>> 
>> The reason why I keep the DNA frozen is that this may reduce the
>> computational cost in two ways:
>> 1. DNA atom coordinates are not updated.
> 
> Frozen groups do not improve performance.
> 
>> 2. Maybe I can have a smaller simulation box (and less number of water
>> molecules), because in principle I can exclude DNA-DNA interactions via
>> energygrp_excl.
>> 
> 
> This is also not true, as there are protein-DNA and protein-water 
> interactions that cannot be ignored.
> 
>> so, I would like to ask you if you think this is a reasonable approach?
>> What could go wrong in such simulations? Any input would be appreciated.
>> 
> 
> Are you sure that there is no potential for the protein to induce any 
> structural change in the DNA?  If you freeze the DNA, you assume that no 
> remodeling occurs.  This assumption could impact the calculated free energy 
> of binding.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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Re: [gmx-users] REMD with Frozen DNA and Moving Protein

[Justin Lemkul]

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 efficiently obtain the free energy landscape of the protein
close to [frozen] DNA.

The reason why I keep the DNA frozen is that this may reduce the
computational cost in two ways:
1. DNA atom coordinates are not updated.


Frozen groups do not improve performance.


2. Maybe I can have a smaller simulation box (and less number of water
molecules), because in principle I can exclude DNA-DNA interactions via
energygrp_excl.



This is also not true, as there are protein-DNA and protein-water interactions 
that cannot be ignored.



so, I would like to ask you if you think this is a reasonable approach?
What could go wrong in such simulations? Any input would be appreciated.



Are you sure that there is no potential for the protein to induce any structural 
change in the DNA?  If you freeze the DNA, you assume that no remodeling occurs. 
 This assumption could impact the calculated free energy of binding.


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] remd jobs failed

[Justin Lemkul]

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:

---
Program g_tune_pme_d, VERSION 4.5.5
Source code file: gmx_tune_pme.c, line: 1579

Fatal error:
File remd_.tpr not found.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


I've got all necessary .tpr file in the same directory (remd_1.tpr, remd_2.tpr
..)



You should be executing mdrun instead of g_tune_pme.

-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] remd jobs failed

[Davide Mercadante]

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"  wrote:

>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 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"  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:
>>>
>>> ---
>>> Program g_tune_pme_d, VERSION 4.5.5
>>> Source code file: gmx_tune_pme.c, line: 1579
>>>
>>> Fatal error:
>>> File remd_.tpr not found.
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> ---
>>>
>>>
>>> I've got all necessary .tpr file in the same directory (remd_1.tpr,
>>> remd_2.tpr ..)
>>>
>>> thank you very much
>>> Albert
>>> -- 
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>>
>
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Re: [gmx-users] remd jobs failed

[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 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"  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:

---
Program g_tune_pme_d, VERSION 4.5.5
Source code file: gmx_tune_pme.c, line: 1579

Fatal error:
File remd_.tpr not found.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


I've got all necessary .tpr file in the same directory (remd_1.tpr,
remd_2.tpr ..)

thank you very much
Albert
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Re: [gmx-users] remd jobs failed

[Davide Mercadante]

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"  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:
>
>---
>Program g_tune_pme_d, VERSION 4.5.5
>Source code file: gmx_tune_pme.c, line: 1579
>
>Fatal error:
>File remd_.tpr not found.
>For more information and tips for troubleshooting, please check the
>GROMACS
>website at http://www.gromacs.org/Documentation/Errors
>---
>
>
>I've got all necessary .tpr file in the same directory (remd_1.tpr,
>remd_2.tpr ..)
>
>thank you very much
>Albert
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Re: [gmx-users] REMD in explicit solvent

[Mark Abraham]

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 there, and then suddently one or a couple of atoms get unstable and
move to much between timesteps.


All the advice of 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation 
and http://www.gromacs.org/Documentation/Terminology/Blowing_Up pertains 
to each individual system for REMD. In particular, you need to 
equilibrate each replica under its conditions and not expect them to 
tolerate a sharp jump in T and to pressure-coupling at the start. The 
fact that you are using gen-vel = yes is proof that you have not 
equilibrated yet :-)



Heres what I have done.

Build the peptide in extended configuration in pymol.
Ran a 200 ps simulation with implicit solvent model to compact the
structure.
Generated a solvent box.
Equilibrated the system for 200 ps.
Generated a range of MDP file with varying temperatures and made
individual .tpr files
Ran the simulation with the switches -multi 16 -replex 1000

I tried to troubleshoot a little with lowering the dt and equilibrating
and minimizing more. Also tried different temperature coupling, as I'm
not sure what is the most appropriate for REMD simulations.


Here's where your background reading comes in ;-) What's good for normal 
simulations is generally good for REMD. There is a school of thought 
that NVT REMD is not good because the pressure is artificially high (but 
I haven't seen anyone demonstrate artefacts from that), but NPT costs 
extra because the volume change affects your PME load balance and accuracy.



Is there something wrong with the parameters of the mdp file?

title= Yo
cpp  = /lib/cpp
include  = -I../top
define   =
integrator   = md
dt   = 0.002
nsteps   = 1000
nstxout  = 1
nstvout  = 1
nstlog   = 1
nstenergy= 1000
nstxtcout= 1000
xtc_grps = Protein
energygrps   = Protein  SOL
nstlist  = 10
ns_type  = grid
rlist= 0.8
coulombtype  = PME
rcoulomb = 0.8


Most would regard this set of PME parameters (most of which are coming 
from defaults) as too cheap to be effective.


Mark


rvdw = 0.8
tcoupl   = Berendsen
tc-grps  = Protein  SOL
tau_t= 0.1  0.1
ref_t= 300  300
Pcoupl   = Berendsen
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0
gen_vel  = yes
gen_temp = 300
gen_seed = 173529
constraints  = all-bonds

Best Regards
Esben





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RE: [gmx-users] REMD question

[Nathalia Garces]

Michael,

Thank you for your answer. On the other hand, I´m not implementing, I´m
using REMD.. I miss wrote it.

Nathalia 

-Mensaje original-
De: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] En
nombre de Michael Shirts
Enviado el: lunes, 28 de mayo de 2012 08:09 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 to be at the equilibrium volume for
your system and temperature choice, which will require equilibration at
constant pressure.

On Mon, May 28, 2012 at 4:37 PM, Nathalia Garces 
wrote:
> 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
>
>
>
>
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Re: [gmx-users] REMD question

[Michael Shirts]

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
equilibration at constant pressure.

On Mon, May 28, 2012 at 4:37 PM, Nathalia Garces  wrote:
> 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
>
>
>
>
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Re: [gmx-users] REMD - low temperature ranges

[Krzysztof Kuczera]

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 sample the folded state. Another 
reason might be having experimental data at lower T, but this
is problematic, as it is hard to model temperature-dependent properties 
with simple force fields.


Krzysztof Kuczera

On 4/27/12 10:06 AM, Tomek Wlodarski wrote:

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 better when you also include lower 
temperature.?

best!

tomek

On Fri, Apr 27, 2012 at 3:40 PM, Mark Abraham > wrote:


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 and I am wondering if
for studing 175 aa protein is better to start from 250K and up
to 350 K or choose from 300-400K (just an example)


Depends on the temperature(s) at which you wish to make
observations. Sampling is normally enhanced at higher
temperatures, so unless you want the ensemble at some low
temperatures, it is normal to start at your lowest observation
temperature.

Of course, you could always read the reasoning provided by the
authors in their paper, or email them for clarification...

Mark
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The University of Kansas
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Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html


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Re: [gmx-users] REMD - low temperature ranges

[Tomek Wlodarski]

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 better when you also include lower temperature.?
best!

tomek

On Fri, Apr 27, 2012 at 3:40 PM, Mark Abraham wrote:

> 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 and I am wondering if for studing
>> 175 aa protein is better to start from 250K and up to 350 K or choose from
>> 300-400K (just an example)
>>
>>
> Depends on the temperature(s) at which you wish to make observations.
> Sampling is normally enhanced at higher temperatures, so unless you want
> the ensemble at some low temperatures, it is normal to start at your lowest
> observation temperature.
>
> Of course, you could always read the reasoning provided by the authors in
> their paper, or email them for clarification...
>
> Mark
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Re: [gmx-users] REMD - low temperature ranges

[Mark Abraham]

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 and I am wondering if for 
studing 175 aa protein is better to start from 250K and up to 350 K or 
choose from 300-400K (just an example)




Depends on the temperature(s) at which you wish to make observations. 
Sampling is normally enhanced at higher temperatures, so unless you want 
the ensemble at some low temperatures, it is normal to start at your 
lowest observation temperature.


Of course, you could always read the reasoning provided by the authors 
in their paper, or email them for clarification...


Mark
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Re: [gmx-users] REMD equilibration

[Erik Marklund]

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 of the simulations under NPT.  At 
> higher temperatures, the box itself may vary more widely and when the system 
> is exchanged, the algorithms can fail.  This phenomenon has been reported by 
> a number of other users.  With NVT, this does not happen.
> 
> -Justin

Very true. The benefit from NPT is on the other hand that the replicas can be 
more distant in temperature space, so if it works then NPT is more efficient.

Erik

> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
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---
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Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
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Re: [gmx-users] REMD equilibration

[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 of the simulations under NPT.  At 
higher temperatures, the box itself may vary more widely and when the system is 
exchanged, the algorithms can fail.  This phenomenon has been reported by a 
number of other users.  With NVT, this does not happen.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] REMD equilibration

[francesco oteri]

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?

Francesco

Il giorno 23 marzo 2012 10:53, Kukol, Andreas  ha
scritto:

> Hi Francesco,
>
> It should be the same 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 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
> or only in the NVT?
>
>
> Thanks in advance, Francesco
> --
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>



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Cordiali saluti, Dr.Oteri Francesco
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RE: [gmx-users] REMD equilibration

[Kukol, Andreas]

Hi Francesco,

It should be the same 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 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 
or only in the NVT?


Thanks in advance, Francesco
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Re: [gmx-users] REMD equilibration

[SebastianWaltz]

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 equilibration has to be carried out in the NPT ensemble
> or only in the NVT?
>
Depends on the ensemble you want to simulate. If the replica you are
interested in should be simulated in NVT you should equilibrate this
replica well and take care that all replicas have the same volume
(meaning that the replicas with higher T have very high pressures). You
also can simulate each replica in an NPT ensemble (and also equilibrate
the replicas with NPT). When the pressure is included in the Metropolis
criteria for the exchange of the trajectories.
> Thanks in advance, Francesco
>
all the best

Sebastian
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Re: [gmx-users] REMD error

[bharat gupta]

The command I used this time :-

mdrun_mpi mdrun -s prefix_.tpr -multi 5 -replex 100


Here's the error that I got :-

Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (5)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Look at these, my work-strong arms" (P.J. Harvey)

Halting program mdrun_mpi

gcq#345: "Look at these, my work-strong arms" (P.J. Harvey)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0


On Thu, Jan 12, 2012 at 3:53 PM, Mark Abraham wrote:

>  On 12/01/2012 5:45 PM, bharat gupta wrote:
>
> It says that "The number of cores must be a multiple of the number of
> replicas (given with -multi, which must equal the number of 
> .tprfiles
>  i.e., 10 for the above general example using
> prefix_0.tpr through prefix_9.tpr)"
>
> I gave the options -multi 5 . But still I am getting the same error. Can
> you please explain, why is it so. Do I need to have the same no. of cores
> as the no. of .tpr files ??
>
>
> You can't be getting an identical error, the numbers are different now.
>
> If mdrun is reporting the number of nodes is 1, then you have not
> configured your MPI environment correctly so that it knows how many
> processors you have available. You will need to solve this by reading your
> MPI documentation.
>
> If you have only four processors, you will not be able to run efficient
> REMD on five replicas, even if you can work out how to get MPI to
> over-allocate MPI processes to your physical processors.
>
> Please copy and paste command line and error together, so that people who
> might help don't feel like they might be wasting their time guessing. They
> have other things to do. Your example input below did not produce your
> error below, because 20 != 3.
>
>
> Mark
>
>
> On Thu, Jan 12, 2012 at 3:38 PM, Mark Abraham wrote:
>
>>  On 12/01/2012 5:29 PM, bharat gupta wrote:
>>
>> Thanks for the advice I re-complied everything again with static
>> libraries and the installation went fine. But while executing the following
>> command I am again getting error :-
>>
>>
>> mdrun_mpi mdrun  -s prefix_.tpr -multi 20 -replex 500 -v
>>
>>
>> Fatal error:
>> The number of nodes (1) is not a multiple of the number of simulations (3)
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>> "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
>>
>> Halting program mdrun_mpi
>>
>> gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
>>
>> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
>>
>>
>> I am trying to simulate 5 replicas and I have 4 cpu .
>>
>>
>>  See http://www.gromacs.org/Documentation/How-tos/REMD Execution Steps
>> point 2. You cannot simulate an arbitrary number of replicas on an
>> arbitrary number of processors.
>>
>> Mark
>>
>>
>>
>>
>>
>> On Thu, Jan 12, 2012 at 1:37 PM, lina  wrote:
>>
>>> 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 loading shared libraries: libgmx_mpi.so.6: cannot
 enable executable stack as shared object requires: Permission denied

>>>
>>>  Can you run a normal md smoothly?
>>> try:
>>> mdrun_mpi mdrun -deffnm prefix_0
>>>
>>> if it works, then some of your trajectories not sound. means system does
>>> not equilibrium well.
>>>
>>>

 Can anybody suggest me how could I rectify this error.

 --
 Bharat


>>>   --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>> --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46...@yahoo.com
>>
>>
>>
>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't po

Re: [gmx-users] REMD error

[Mark Abraham]

On 12/01/2012 5:45 PM, bharat gupta wrote:
It says that "The number of cores must be a multiple of the number of 
replicas (given with |-multi|, which must equal the number of .tpr 
 
files i.e., 10 for the above general example using |prefix_0.tpr| 
through |prefix_9.tpr|)"


I gave the options -multi 5 . But still I am getting the same error. 
Can you please explain, why is it so. Do I need to have the same no. 
of cores as the no. of .tpr files ??


You can't be getting an identical error, the numbers are different now.

If mdrun is reporting the number of nodes is 1, then you have not 
configured your MPI environment correctly so that it knows how many 
processors you have available. You will need to solve this by reading 
your MPI documentation.


If you have only four processors, you will not be able to run efficient 
REMD on five replicas, even if you can work out how to get MPI to 
over-allocate MPI processes to your physical processors.


Please copy and paste command line and error together, so that people 
who might help don't feel like they might be wasting their time 
guessing. They have other things to do. Your example input below did not 
produce your error below, because 20 != 3.


Mark



On Thu, Jan 12, 2012 at 3:38 PM, Mark Abraham > wrote:


On 12/01/2012 5:29 PM, bharat gupta wrote:

Thanks for the advice I re-complied everything again with static
libraries and the installation went fine. But while executing the
following command I am again getting error :-


mdrun_mpi mdrun  -s prefix_.tpr -multi 20 -replex 500 -v


Fatal error:
The number of nodes (1) is not a multiple of the number of
simulations (3)
For more information and tips for troubleshooting, please check
the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)

Halting program mdrun_mpi

gcq#155: "BioBeat is Not Available In Regular Shops" (P.J.
Meulenhoff)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0


I am trying to simulate 5 replicas and I have 4 cpu .


See http://www.gromacs.org/Documentation/How-tos/REMD Execution
Steps point 2. You cannot simulate an arbitrary number of replicas
on an arbitrary number of processors.

Mark






On Thu, Jan 12, 2012 at 1:37 PM, lina mailto:lina.lastn...@gmail.com>> wrote:

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 loading shared libraries:
libgmx_mpi.so.6: cannot
enable executable stack as shared object requires:
Permission denied


Can you run a normal md smoothly?
try:
mdrun_mpi mdrun -deffnm prefix_0

if it works, then some of your trajectories not sound. means
system does not equilibrium well.



Can anybody suggest me how could I rectify this error.

--
Bharat


-- 
gmx-users mailing list gmx-users@gromacs.org


http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
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-- 
Bharat

Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 






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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering an

Re: [gmx-users] REMD error

[bharat gupta]

It says that "The number of cores must be a multiple of the number of
replicas (given with -multi, which must equal the number of
.tprfiles
i.e., 10 for the above general example using
prefix_0.tpr through prefix_9.tpr)"

I gave the options -multi 5 . But still I am getting the same error. Can
you please explain, why is it so. Do I need to have the same no. of cores
as the no. of .tpr files ??

On Thu, Jan 12, 2012 at 3:38 PM, Mark Abraham wrote:

>  On 12/01/2012 5:29 PM, bharat gupta wrote:
>
> Thanks for the advice I re-complied everything again with static libraries
> and the installation went fine. But while executing the following command I
> am again getting error :-
>
>
> mdrun_mpi mdrun  -s prefix_.tpr -multi 20 -replex 500 -v
>
>
> Fatal error:
> The number of nodes (1) is not a multiple of the number of simulations (3)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
>
> Halting program mdrun_mpi
>
> gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
>
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
>
>
> I am trying to simulate 5 replicas and I have 4 cpu .
>
>
> See http://www.gromacs.org/Documentation/How-tos/REMD Execution Steps
> point 2. You cannot simulate an arbitrary number of replicas on an
> arbitrary number of processors.
>
> Mark
>
>
>
>
>
> On Thu, Jan 12, 2012 at 1:37 PM, lina  wrote:
>
>> 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 loading shared libraries: libgmx_mpi.so.6: cannot
>>> enable executable stack as shared object requires: Permission denied
>>>
>>
>>  Can you run a normal md smoothly?
>> try:
>> mdrun_mpi mdrun -deffnm prefix_0
>>
>> if it works, then some of your trajectories not sound. means system does
>> not equilibrium well.
>>
>>
>>>
>>> Can anybody suggest me how could I rectify this error.
>>>
>>> --
>>> Bharat
>>>
>>>
>>   --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46...@yahoo.com
>
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Re: [gmx-users] REMD error

[Mark Abraham]

On 12/01/2012 5:29 PM, bharat gupta wrote:
Thanks for the advice I re-complied everything again with static 
libraries and the installation went fine. But while executing the 
following command I am again getting error :-



mdrun_mpi mdrun  -s prefix_.tpr -multi 20 -replex 500 -v


Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (3)
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---

"BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)

Halting program mdrun_mpi

gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0


I am trying to simulate 5 replicas and I have 4 cpu .


See http://www.gromacs.org/Documentation/How-tos/REMD Execution Steps 
point 2. You cannot simulate an arbitrary number of replicas on an 
arbitrary number of processors.


Mark





On Thu, Jan 12, 2012 at 1:37 PM, lina > wrote:


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 loading shared libraries:
libgmx_mpi.so.6: cannot
enable executable stack as shared object requires: Permission
denied


Can you run a normal md smoothly?
try:
mdrun_mpi mdrun -deffnm prefix_0

if it works, then some of your trajectories not sound. means
system does not equilibrium well.



Can anybody suggest me how could I rectify this error.

--
Bharat


-- 
gmx-users mailing list gmx-users@gromacs.org


http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 





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Re: [gmx-users] REMD error

[bharat gupta]

Thanks for the advice I re-complied everything again with static libraries
and the installation went fine. But while executing the following command I
am again getting error :-


mdrun_mpi mdrun  -s prefix_.tpr -multi 20 -replex 500 -v


Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (3)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)

Halting program mdrun_mpi

gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0


I am trying to simulate 5 replicas and I have 4 cpu .



On Thu, Jan 12, 2012 at 1:37 PM, lina  wrote:

> 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 loading shared libraries: libgmx_mpi.so.6: cannot
>> enable executable stack as shared object requires: Permission denied
>>
>
> Can you run a normal md smoothly?
> try:
> mdrun_mpi mdrun -deffnm prefix_0
>
> if it works, then some of your trajectories not sound. means system does
> not equilibrium well.
>
>
>>
>> Can anybody suggest me how could I rectify this error.
>>
>> --
>> Bharat
>>
>>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] REMD error

[lina]

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 loading shared libraries: libgmx_mpi.so.6: cannot
enable executable stack as shared object requires: Permission denied


Can you run a normal md smoothly?
try:
mdrun_mpi mdrun -deffnm prefix_0

if it works, then some of your trajectories not sound. means system does 
not equilibrium well.



Can anybody suggest me how could I rectify this error.

--
Bharat



--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] REMD error

[Mark Abraham]

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 libraries: libgmx_mpi.so.6: 
cannot enable executable stack as shared object requires: Permission 
denied




You configured GROMACS to use shared libraries, but something about them 
or your current environment doesn't work. Try rebuilding GROMACS, 
building with static libraries, or discussing with your system admins.


Mark
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Re: [gmx-users] remd in the npt ensemble: When the exchange, the temperature abruptly surge .

[Mark Abraham]

On 28/11/2011 10:37 PM, ?? wrote:

dear teacher,
i find the answer of that  letter "Subject: Re: [gmx-users] REMD: NPT 
being +-Infinity or NaN",
ifind that "when the exchange, the temperature abruptly surge .",as 
follows,

dt=0.002ps  -replex 4000

@ s0 legend "Temperature"
@ s1 legend "Pressure"
0.00  546.497375   60.637791
1.00  556.582397  244.328201
..
   94.00  557.564453  -17.035589
   95.00  543.882629   57.111996
   96.00  523.336548  -25.745819
   97.00  555.043335  254.709778
   98.00  555.595886  -39.830761
   99.00  542.395325   49.084045
  100.00  550.955261  -149.259979
  101.00  134372.953125  4419.518066
  102.00  156382.859375  -17109.099609
  103.00  138660.156250  -11395.237305
  104.00  165148.265625  20807.541016
...

But if change the replex to 4,so i can not exchange.
Then the system is ok.
&& The initial conformation has been done a long time MD


If this is the same system as previously reported, then you're probably 
observing the system velocities exploding on one replica then being 
exchanged to a new replica.


Mark



thanks for your help !!
Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303 ; +8613820062885
E-mail: 2008d...@gmail.com <mailto:2008d...@gmail.com> ; 
dubo2...@tju.edu.cn <mailto:dubo2...@tju.edu.cn>






===
Message: 4
Date: Sun, 27 Nov 2011 22:36:08 -0500
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] REMD: NPT being +-Infinity or NaN
To: Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>>

Message-ID: <4ed301a8.9070...@vt.edu <mailto:4ed301a8.9070...@vt.edu>>
Content-Type: text/plain; charset=UTF-8; format=flowed



?? wrote:
> dear teacher,
> when i do remd  in the  npt ensemble.
>
> REMD: NPT -replex 4000
> dt= 0.0001
>
> step 172000, will finish Sat Dec 31 18:44:12 2011
>
> ---
> Program mdrun_mpi_4.5.5, VERSION 4.5.5
> Source code file: nsgrid.c, line: 549
>
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with 
some

> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
>
> how could  i do except using the small dt ?
>

Your system is not stable, as is often the case with NPT REMD at high 
temperature.


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] REMD: NPT being +-Infinity or NaN

[Justin A. Lemkul]

杜波 wrote:

dear teacher,
when i do remd  in the  npt ensemble.

REMD: NPT -replex 4000
dt= 0.0001

step 172000, will finish Sat Dec 31 18:44:12 2011

---
Program mdrun_mpi_4.5.5, VERSION 4.5.5
Source code file: nsgrid.c, line: 549

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

how could  i do except using the small dt ? 



Your system is not stable, as is often the case with NPT REMD at high 
temperature.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] REMD: when it exchange the replica, it will be bombed!!

[Mark Abraham]

On 19/11/2011 1:49 PM, 杜波 wrote:

dear teachear,
i do remd in NPT,
when it exchange the replica, it will be bombed!!

step 400, will finish Wed Nov 23 23:21:34 2011
Warning: 1-4 interaction between 1384 and 1396 at distance 140.157 
which is larger than the 1-4 table size 20.895 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

---
Program mdrun_mpi_4.5.5, VERSION 4.5.5
Source code file: nsgrid.c, line: 549

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value 175. It should have been within [ 0 .. 168 ]

For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors



Did you check out the information available for this issue there? Does 
your simulation even run without REMD?


Mark
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Re: [gmx-users] remd :One of the processes started by mpirun has exited with a nonzero exit code.

[Mark Abraham]

On 14/11/2011 12:29 AM, 杜波 wrote:

dear teacher
when i do remd , i got an erro ! bu i do not know how to do !
thanks!!!

modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

:-) /export/software/bin/mdrun_mpi_4.5.5 (-:

Option Filename Type Description

-s pmma.tpr Input Run input file: tpr tpb tpa
-o md.trr Output Full precision trajectory: trr trj cpt
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi state.cpt Input, Opt. Checkpoint file
-cpo state.cpt Output, Opt. Checkpoint file
-c after_md.gro Output Structure file: gro g96 pdb etc.
-e ener.edr Output Energy file
-g md.log Output Log file
-dhdl dhdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-tableb table.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi tpi.xvg Output, Opt. xvgr/xmgr file
-tpid tpidist.xvg Output, Opt. xvgr/xmgr file
-ei sam.edi Input, Opt. ED sampling input
-eo sam.edo Output, Opt. ED sampling output
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-px pullx.xvg Output, Opt. xvgr/xmgr file
-pf pullf.xvg Output, Opt. xvgr/xmgr file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file
-multidir ./0/ Input, Opt!, Mult.
./1/
./2/
./3/
./4/
./5/
./6/
./7/
./8/
./9/
./10/
./11/ Run directory

Option Type Value Description
--
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool yes Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 2000 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system

NNODES=12, MYRANK=7, HOSTNAME=c0115
NNODES=12, MYRANK=1, HOSTNAME=c0101
NNODES=12, MYRANK=2, HOSTNAME=c0101
NODEID=1 argc=26
NNODES=12, MYRANK=5, HOSTNAME=c0113
NNODES=12, MYRANK=6, HOSTNAME=c0113
NODEID=5 argc=26
NNODES=12, MYRANK=3, HOSTNAME=c0102
NNODES=12, MYRANK=4, HOSTNAME=c0102
NODEID=3 argc=26
NODEID=2 argc=26
NODEID=6 argc=26
NODEID=4 argc=26
NNODES=12, MYRANK=9, HOSTNAME=c0115
NNODES=12, MYRANK=11, HOSTNAME=c0115
NODEID=11 argc=26
NODEID=7 argc=26
NNODES=12, MYRANK=8, HOSTNAME=c0115
NODEID=8 argc=26
NNODES=12, MYRANK=10, HOSTNAME=c0115
NODEID=9 argc=26
NODEID=10 argc=26

Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file pmma.tpr, VERSION 4.5.5 (single precision)

Back Off! I just backed up md.log to ./#md.log.1#

Back Off! I just backed up md.log to ./#md.log.1#

Back Off! I just backed up md.log to ./#md.log.1#

Back Off! I just backed up md.log to ./#md.log.1#

Back Off! I just backed up md.log to ./#md.log.1#

Back Off! I just backed up md.log to ./#md.log.1#

Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Getting Loaded...
Loaded with Money

Getting Loaded...
Reading file pmma.tpr, VERSION 4.5.5 (single precision)
Reading file pmma.tpr, VERSION 4.5.5 (single precision)
Reading file pmma.tpr, VERSION 4.5.5 (single precision)
Getting Loaded...
Getting Loaded.

Re: Re: [gmx-users] remd with different potential at different temperature

[Roland Schulz]

Hi,

this is currently not possible. Currently you can only do temperature or
Hamiltonian RepEx. As far as I know 4.6 will support both simultaneous. In
the mean time you might be able to accomplish your goal
by reformulating the Temp-RepEx as a Hamiltonian RepEx as is done in the
newer version of REST.

Roland

2011/11/8 杜波 <2008d...@gmail.com>

>  dear teacher,
> if i want to do remd  with different tabulated potentials.
> how can i use the mdrun's   -table (-table table.xvg -tableb table.xvg )?
> if it can also use like that,there is another question:
> and how can i rename the tables name ( table_CR1_CR1: i rename
> them table_CR1_CR10,table_CR1_CR11,table_CR1_CR12...,
> i test this is wrong!!!
>  )
> thanks
> > regards,
> > PHD, Bo Du
> > Department of Polymer Science and Engineering,
> > School of Chemical Engineering and technology,
> > Tianjin University, Weijin Road 92, Nankai District 300072,
> > Tianjin City P. R. China
> > Tel/Fax: +86-22-27404303
> > E-mail: 2008d...@gmail.com <mailto:2008d...@gmail.com>
>
>
>
>
>
>  Message: 1
> Date: Tue, 08 Nov 2011 17:55:49 +1100
> From: Mark Abraham 
> Subject: Re: [gmx-users] remd with different potential at different
>temperature
> To: Discussion list for GROMACS users 
> Message-ID: <4eb8d275.2010...@anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> On 8/11/2011 5:43 PM, ?? wrote:
> > dear teacher,
> > how can i do remd with different non-bond potential at different
> > temperature ?
> > easy to say ,can i use different *.top at diferent temperature.
>
> Probably. Try a simple case and see. The REMD implementation checks only
> certain critical quantities are constant over the generalized ensemble.
> See the lines that begin "Multi-checking" in an REMD .log file. You can
> probably even use different tabulated potentials for each replica.
>
> Mark
>
> >
> > if not ,can you give me some suggestions to rewrite the gromacs codes.
> > thanks!!
> >
> > regards,
> > PHD, Bo Du
> > Department of Polymer Science and Engineering,
> > School of Chemical Engineering and technology,
> > Tianjin University, Weijin Road 92, Nankai District 300072,
> > Tianjin City P. R. China
> > Tel/Fax: +86-22-27404303
> > E-mail: 2008d...@gmail.com <mailto:2008d...@gmail.com>
> >
> >
> >
>



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Re: [gmx-users] remd with different potential at different temperature

[Mark Abraham]

On 8/11/2011 5:43 PM, ?? wrote:

dear teacher,
how can i do remd with different non-bond potential at different 
temperature ?

easy to say ,can i use different *.top at diferent temperature.


Probably. Try a simple case and see. The REMD implementation checks only 
certain critical quantities are constant over the generalized ensemble. 
See the lines that begin "Multi-checking" in an REMD .log file. You can 
probably even use different tabulated potentials for each replica.


Mark



if not ,can you give me some suggestions to rewrite the gromacs codes.
thanks!!

regards,
PHD, Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303
E-mail: 2008d...@gmail.com 





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Re: [gmx-users] remd- Function not implemented

[Mark Abraham]

On 3/11/2011 6:15 PM, 杜波 wrote:

Dear teacher,
when i do remd , the power is off . Then i use the commd
"
to=21
lamboot
mpirun_lam -np $to mdrun_mpi_4.5 -multi $to -replex 100 -nice 0 -cpi 
state.cpt -s pmma.tpr -o md -c after_md -v

"
to continue to run the progarm.
But there is a Fatal error!!

Program mdrun_mpi_4.5, VERSION 4.5.5
Source code file: checkpoint.c, line: 1757

Fatal error:
Failed to lock: md15.log. Function not implemented.
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors



lam is unsuitable for GROMACS because it does not implement the 
functionality required. openmpi is suggested.


Mark
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Re: [gmx-users] REMD output

[Mark Abraham]

On 19/10/2011 9:55 PM, Wright, Louise wrote:


Dear all,
I want to double check, the output from an REMD simulation with 
Gromacs is the trajectory at constant Temp and whe you demux it with 
demux.pl, this is the trajectory of the replica which starts at a 
given tempurature and how it evolves through time?




Correct.

Mark

For instance, if _0.tpr file corresponds to temp of 300K then the 
traj_0.xtc will be the trajectory structures all at temp 300K and 
after demuxing, a different file labelled for example 0_final_traj.xtc 
is not at constant temp.

Thanks for the help
Louise







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Re: [gmx-users] REMD and GBSA

[Mark Abraham]

On 18/10/2011 4:58 AM, Ben Reynwar wrote:

On Fri, Oct 14, 2011 at 9:11 AM, Mark Abraham  wrote:

On 14/10/2011 10:12 AM, Ben Reynwar wrote:

Hi gromacs list,

I'm about to start some REMD simulations using generalized Born
solvent on a protein of about 5000 atoms.  I have two questions, the
first of which is about gromacs, the second more about REMD in
general.

(1)
I'm getting some pretty ugly energy drift (300K->500K in 1 ns) for an
NVE MD test simulation using a 2 fs time step.  It goes away if I use
1 fs, however I was under the impression that 2 fs is normally OK.  I
was wondering whether that could be caused by the use of the cut-off
method which is required with the coloumb and VdW interactions when
using GBSA?  Or perhaps I'm doing something else wrong.  I'll include
the mdp file I'm using at the bottom of the email in case anyone feels
like pointing out my foolishness to me.

Drift is normal if you use 2fs with hbond constraints. all-bond constraints
are necessary for 2fs.


Great. Thank you.


(2)
I've been analyzing some data from an REMD simulation by my
predecessor and see very slow replica flow rates.  They are about two
orders of magnitude smaller than the idealized rate of the exchange
attempt frequency multiplied by the acceptance fraction (exchanges are
attempted every 2 ps with a 0.4 acceptance fraction).  If I look at
the energy distribution for a given replica/temperature combination
over a time scale of around 1 ns, it is clearly shifted from the
average energy distribution for that temperature.  The timescale for
changes in this energy shift is around 10 ns.  My current theory for
the slow rate of replica flow is that the slow fluctuations in the
energy of the protein are limiting replica flow, since a replica with
lower than average energy will tend to remain at the bottom of the
temperature range, while those with higher than average energies will
tend to remain at the top.  Has anyone else observed this kind of
behavior?  Is my reasoning wrong in any obvious way?

A replica with "lower than average energy" *for that temperature* will tend
to drift down the temperature ladder in favour of another.

One can observe blockages in replica flow. If all the replicas below a given
temperature are in regions of configuration space that cannot access PE high
enough to have a significant chance of exchanging above that temperature,
then flow does not occur (and vice-versa, of course). If one were to sample
a FES that had two minima that should be sampled in a 2:1 ratio, but started
from a 1:1 ratio and did not have a high enough temperature range to cross
the barrier, then the exchange acceptance rate can look good when nothing
useful is occurring - the observation will necessarily be that these minima
are equally likely. The two groups are actually engaging in disjoint flow,
and one needs to look at metrics other than the acceptance rate to observe
it. The only way to deal with such a bottleneck is to have replicas at a
high enough temperature that both groups can exchange to those temperatures
- only now can barrier crossing occur. These kinds of phenomena can
certainly occur over short time scales in localized regions of configuration
and temperature space.

Mark


Do you know if anyone has done any studies looking at replica flow in
well-defined, comparatively low-dimensional landscapes to get a
qualitative feel for these kinds of effects?  It would be interesting
to see what effect replica exchange settings can have on replica flow
beyond the simple random walk models, when you take into account the
fact that different regions of configuration space could have
different potential energy distributions for the same temperature.



See for example Walter Nadler, Jan H. Meinke, and Ulrich H. E. Hansmann 
"Folding proteins by first-passage-times-optimized replica exchange", 
PHYSICAL REVIEW E 78, 061905, 2008 (and related work)


Mark
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Re: [gmx-users] REMD and GBSA

[Ben Reynwar]

On Fri, Oct 14, 2011 at 9:11 AM, Mark Abraham  wrote:
> On 14/10/2011 10:12 AM, Ben Reynwar wrote:
>>
>> Hi gromacs list,
>>
>> I'm about to start some REMD simulations using generalized Born
>> solvent on a protein of about 5000 atoms.  I have two questions, the
>> first of which is about gromacs, the second more about REMD in
>> general.
>>
>> (1)
>> I'm getting some pretty ugly energy drift (300K->500K in 1 ns) for an
>> NVE MD test simulation using a 2 fs time step.  It goes away if I use
>> 1 fs, however I was under the impression that 2 fs is normally OK.  I
>> was wondering whether that could be caused by the use of the cut-off
>> method which is required with the coloumb and VdW interactions when
>> using GBSA?  Or perhaps I'm doing something else wrong.  I'll include
>> the mdp file I'm using at the bottom of the email in case anyone feels
>> like pointing out my foolishness to me.
>
> Drift is normal if you use 2fs with hbond constraints. all-bond constraints
> are necessary for 2fs.
>
Great. Thank you.

>>
>> (2)
>> I've been analyzing some data from an REMD simulation by my
>> predecessor and see very slow replica flow rates.  They are about two
>> orders of magnitude smaller than the idealized rate of the exchange
>> attempt frequency multiplied by the acceptance fraction (exchanges are
>> attempted every 2 ps with a 0.4 acceptance fraction).  If I look at
>> the energy distribution for a given replica/temperature combination
>> over a time scale of around 1 ns, it is clearly shifted from the
>> average energy distribution for that temperature.  The timescale for
>> changes in this energy shift is around 10 ns.  My current theory for
>> the slow rate of replica flow is that the slow fluctuations in the
>> energy of the protein are limiting replica flow, since a replica with
>> lower than average energy will tend to remain at the bottom of the
>> temperature range, while those with higher than average energies will
>> tend to remain at the top.  Has anyone else observed this kind of
>> behavior?  Is my reasoning wrong in any obvious way?
>
> A replica with "lower than average energy" *for that temperature* will tend
> to drift down the temperature ladder in favour of another.
>
> One can observe blockages in replica flow. If all the replicas below a given
> temperature are in regions of configuration space that cannot access PE high
> enough to have a significant chance of exchanging above that temperature,
> then flow does not occur (and vice-versa, of course). If one were to sample
> a FES that had two minima that should be sampled in a 2:1 ratio, but started
> from a 1:1 ratio and did not have a high enough temperature range to cross
> the barrier, then the exchange acceptance rate can look good when nothing
> useful is occurring - the observation will necessarily be that these minima
> are equally likely. The two groups are actually engaging in disjoint flow,
> and one needs to look at metrics other than the acceptance rate to observe
> it. The only way to deal with such a bottleneck is to have replicas at a
> high enough temperature that both groups can exchange to those temperatures
> - only now can barrier crossing occur. These kinds of phenomena can
> certainly occur over short time scales in localized regions of configuration
> and temperature space.
>
> Mark
>

Do you know if anyone has done any studies looking at replica flow in
well-defined, comparatively low-dimensional landscapes to get a
qualitative feel for these kinds of effects?  It would be interesting
to see what effect replica exchange settings can have on replica flow
beyond the simple random walk models, when you take into account the
fact that different regions of configuration space could have
different potential energy distributions for the same temperature.

Cheers,
Ben

>>
>> Cheers,
>> Ben
>>
>> ; An energy drift simulation of TaHSP.
>>
>> ; 7.3.2 Preprocssing
>> ; --
>> ; defines pass to the preprocessor
>> define =
>>
>> ; 7.3.3 Run Control
>> ; -
>> ; group(s) for center of mass motion removal
>> comm_grps = System
>> ; Use the MD integrator (as opposed to minimization).
>> integrator = md
>> ; maximum number of steps to integrate
>> nsteps = 1
>> ; remove center of mass translation and rotation around centre of mass
>> comm_mode = Angular
>> ; [ps] time step for integration
>> dt = 0.002
>> ; [steps] frequency of mass motion removal
>> nstcomm = 10
>> ; [ps] starting time for run
>> tinit = 0
>>
>> ; 7.3.8 Output Control
>> ; 
>> ; [steps] freq to write velocities to trajectory
>> nstvout = 0
>> ; [steps] freq to write energies to log file
>> nstlog = 100
>> ; Write to energy file frequently.
>> nstenergy = 100
>> ; group(s) to write to xtc trajectory
>> xtc_grps = System
>> ; [real] precision to write xtc trajectory
>> xtc_precision = 1000
>> ; [steps] freq to write coordinates to xtc trajectory
>> nstxtcout = 1000
>> ; [steps] freq to write coordinates to

Re: [gmx-users] REMD and GBSA

[Mark Abraham]

On 14/10/2011 10:12 AM, Ben Reynwar wrote:

Hi gromacs list,

I'm about to start some REMD simulations using generalized Born
solvent on a protein of about 5000 atoms.  I have two questions, the
first of which is about gromacs, the second more about REMD in
general.

(1)
I'm getting some pretty ugly energy drift (300K->500K in 1 ns) for an
NVE MD test simulation using a 2 fs time step.  It goes away if I use
1 fs, however I was under the impression that 2 fs is normally OK.  I
was wondering whether that could be caused by the use of the cut-off
method which is required with the coloumb and VdW interactions when
using GBSA?  Or perhaps I'm doing something else wrong.  I'll include
the mdp file I'm using at the bottom of the email in case anyone feels
like pointing out my foolishness to me.


Drift is normal if you use 2fs with hbond constraints. all-bond 
constraints are necessary for 2fs.




(2)
I've been analyzing some data from an REMD simulation by my
predecessor and see very slow replica flow rates.  They are about two
orders of magnitude smaller than the idealized rate of the exchange
attempt frequency multiplied by the acceptance fraction (exchanges are
attempted every 2 ps with a 0.4 acceptance fraction).  If I look at
the energy distribution for a given replica/temperature combination
over a time scale of around 1 ns, it is clearly shifted from the
average energy distribution for that temperature.  The timescale for
changes in this energy shift is around 10 ns.  My current theory for
the slow rate of replica flow is that the slow fluctuations in the
energy of the protein are limiting replica flow, since a replica with
lower than average energy will tend to remain at the bottom of the
temperature range, while those with higher than average energies will
tend to remain at the top.  Has anyone else observed this kind of
behavior?  Is my reasoning wrong in any obvious way?


A replica with "lower than average energy" *for that temperature* will 
tend to drift down the temperature ladder in favour of another.


One can observe blockages in replica flow. If all the replicas below a 
given temperature are in regions of configuration space that cannot 
access PE high enough to have a significant chance of exchanging above 
that temperature, then flow does not occur (and vice-versa, of course). 
If one were to sample a FES that had two minima that should be sampled 
in a 2:1 ratio, but started from a 1:1 ratio and did not have a high 
enough temperature range to cross the barrier, then the exchange 
acceptance rate can look good when nothing useful is occurring - the 
observation will necessarily be that these minima are equally likely. 
The two groups are actually engaging in disjoint flow, and one needs to 
look at metrics other than the acceptance rate to observe it. The only 
way to deal with such a bottleneck is to have replicas at a high enough 
temperature that both groups can exchange to those temperatures - only 
now can barrier crossing occur. These kinds of phenomena can certainly 
occur over short time scales in localized regions of configuration and 
temperature space.


Mark



Cheers,
Ben

; An energy drift simulation of TaHSP.

; 7.3.2 Preprocssing
; --
; defines pass to the preprocessor
define =

; 7.3.3 Run Control
; -
; group(s) for center of mass motion removal
comm_grps = System
; Use the MD integrator (as opposed to minimization).
integrator = md
; maximum number of steps to integrate
nsteps = 1
; remove center of mass translation and rotation around centre of mass
comm_mode = Angular
; [ps] time step for integration
dt = 0.002
; [steps] frequency of mass motion removal
nstcomm = 10
; [ps] starting time for run
tinit = 0

; 7.3.8 Output Control
; 
; [steps] freq to write velocities to trajectory
nstvout = 0
; [steps] freq to write energies to log file
nstlog = 100
; Write to energy file frequently.
nstenergy = 100
; group(s) to write to xtc trajectory
xtc_grps = System
; [real] precision to write xtc trajectory
xtc_precision = 1000
; [steps] freq to write coordinates to xtc trajectory
nstxtcout = 1000
; [steps] freq to write coordinates to trajectory
nstxout = 0
; group(s) to write to energy file
energygrps = System
; [steps] freq to write forces to trajectory
nstfout = 0

; 7.3.9 Neighbour Searching
; -
; [nm] cut-off distance for the short-range neighbor list
; For Generalized Born this must be equal to the cut-off length for
; the born radius calculation.
rlist = 1.6
; method of updating neighbor list
ns_type = grid
; [steps] freq to update neighbor list
nstlist = 1
; no periodic boundary conditions
pbc = no

; 7.3.10 Electrostatics
; -
; apply a cut-off to electostatic
coulombtype = cut-off
; coloumb cutoff radius
rcoulomb = 1.6

; 7.3.11 VdW
; --
; Dispersion correction makes no sense without box size.
DispCorr = no
; twin-range cut-off with rlist where rvdw>rlist
vdwtype 

Re: [gmx-users] REMD problem

[Justin A. Lemkul]

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 coordinates along each trajectory 
(ensemble-continuous), and the final snapshot is written to a .gro file by mdrun 
(although these do not necessarily tell you anything by themselves).



I am totally fresh to MD simulation, just worked on this for 1 week ...



Back up.  REMD can be very complex, especially if you want to do it right.  Do 
some basic tutorial material (standard MD) and understand the workflow and 
analysis.  Spend time in the literature, as Mark suggested.  The time investment 
you make now may delay your actual data collection by a few weeks, but will save 
you months of wasted time overall if you try to plow ahead without a clear 
vision for what you're doing.


-Justin

On Thu, Sep 29, 2011 at 4:24 PM, Mark Abraham > wrote:


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 you have made a
number of totally arbitrary choices.



I tried to analyze the result, and after applying demux.pl
, two files replica_index.xvg  replica_temp.xvg
are obtained.


Why did you want to demux?



My question is how to obtain the structure information? (I will
need pdb file).


Do all the tutorial material you can find - even if not strictly
relevant - to get an idea about good workflows. Then try to
replicate (part of) a published REMD study to see how things work
there. Search the web and check out the GROMACS web page - there's
lots of material out there. Stabbing in the dark is a great way to
waste your time, and people here don't have the time to teach every
person every thing.

Mark

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--
Best,
Liang Liu



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] REMD problem

[Liu, Liang]

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, Sep 29, 2011 at 4:24 PM, Mark Abraham wrote:

>  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 you have made a number
> of totally arbitrary choices.
>
>
>  I tried to analyze the result, and after applying demux.pl, two
> files replica_index.xvg  replica_temp.xvg are obtained.
>
>
> Why did you want to demux?
>
>
>  My question is how to obtain the structure information? (I will need pdb
> file).
>
>
> Do all the tutorial material you can find - even if not strictly relevant -
> to get an idea about good workflows. Then try to replicate (part of) a
> published REMD study to see how things work there. Search the web and check
> out the GROMACS web page - there's lots of material out there. Stabbing in
> the dark is a great way to waste your time, and people here don't have the
> time to teach every person every thing.
>
> Mark
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Best,
Liang Liu
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] REMD problem

[Mark Abraham]

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 you have made a 
number of totally arbitrary choices.


I tried to analyze the result, and after applying demux.pl 
, two files replica_index.xvg  replica_temp.xvg are 
obtained.


Why did you want to demux?

My question is how to obtain the structure information? (I will need 
pdb file).


Do all the tutorial material you can find - even if not strictly 
relevant - to get an idea about good workflows. Then try to replicate 
(part of) a published REMD study to see how things work there. Search 
the web and check out the GROMACS web page - there's lots of material 
out there. Stabbing in the dark is a great way to waste your time, and 
people here don't have the time to teach every person every thing.


Mark
-- 
gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] REMD problem

[Liu, Liang]

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 question is how to obtain the structure information? (I will need pdb
file).
-- 
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Re: [gmx-users] REMD problem

[Liu, Liang]

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 question is how to obtain the structure information? (I will need pdb
file).

On Thu, Sep 29, 2011 at 6:23 AM, Manuel Prinz wrote:

> 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
> idea is left on as an exercise to the reader. ;)
>
> Best regards,
> Manuel
>
> [1] When not run from a resource manager that takes care of setting the
> "right" configuration options.
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Best,
Liang Liu
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] REMD problem

[Manuel Prinz]

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
idea is left on as an exercise to the reader. ;)

Best regards,
Manuel

[1] When not run from a resource manager that takes care of setting the
"right" configuration options.

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Re: [gmx-users] REMD problem

[Liu, Liang]

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 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 44   45 x 46   47   48   49
>>> Repl pr1.0   1.0   1.0   .00   1.0   1.0
>>>   .00   1.0   1.0   1.0   1.0   .00   1.0   .00
>>>   1.0   .00   1.0   .00   .46   .00   1.0
>>> .78   1.0   .00
>>>
>>> Replica exchange at step 5750 time 11.5
>>> Repl 0 <-> 1  dE = -7.583e+00
>>> Repl ex  0 x  1234 x  56 x  78 x  9   10 x 11   12 x
>>> 13   14 x 15   16 x 17   18 x 19   20   21   22   23   24 x 25   26   27
>>> 28 x 29   30   31   32 x 33   34   35   36   37   38   39   40 x 41   42 x
>>> 43   44   45   46   47   48   49
>>> Repl pr   1.0   .00   1.0   1.0   1.0   1.0   1.0
>>>   1.0   1.0   1.0   .48   .11   1.0   .00
>>> 1.0   .00   1.0   .00   .00   .01   1.0   1.0
>>> .00   .01   .01
>>>
>>>   Step   Time Lambda
>>>   5800   11.60.0
>>>
>>>   Energies (kJ/mol)
>>>  AngleProper Dih.  Improper Dih.  LJ-14
>>> Coulomb-14
>>>9.69806e+021.32207e+033.34938e+014.93171e+02
>>> -3.9e+03
>>>LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position
>>> Rest.
>>>3.14374e+04   -6.42258e+02   -1.88529e+05   -2.01604e+04
>>>  0.0e+00
>>>  PotentialKinetic En.   Total Energy  Conserved En.
>>>  Temperature
>>>   -1.78987e+054.57462e+04   -1.33240e+051.23302e+10
>>>  5.62201e+02
>>>  Pres. DC (bar) Pressure (bar)   Constr. rmsd
>>>   -2.12803e+02   -5.47109e+022.21484e-05
>>> ...
>>>
>>>
>> Perhaps someone else can offer an explanation.  It should not be possible
>> to run multiple replicas on a single processor.  Also note that your
>> exchange probability is extremely high; you're likely not obtaining
>> meaningful sampling.
>>
>
> If the MPI configuration allows physical processors to be over-allocated,
> then GROMACS is none the wiser.
>
> Mark
>
>
>
>> -Justin
>>
>>  On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>>
>>>
>>>
>>>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 cannot
>>>think of a reason why 50 simulations could possibly run on 2
>>> processors.
>>>
>>>-Justin
>>>
>>>On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul
>>> mailto:jalem...@vt.edu>
>>> >> wrote:
>>>
>>>
>>>
>>>   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 are actually running, or at the very
>>> least
>>>   you will get horribly slow performance.
>>>
>>>
>>>   By the way, would you please show me where I can find the
>>>   reasonable replex number information in the literature?
>>> I did
>>>   not find it in the link you posted and the manual either.
>>>
>>>
>>>   A few minutes of real literature searching will be far more
>>>valuable
>>>   than some random person on the Internet giving you a value
>>>that you
>>>   blindly use ;)
>>>
>>>   -Justin
>>>
>>>   Thanks.
>>>
>>>
>>>   -- Best,
>>>   Liang Liu
>>>
>>>
>>>   -- ==**==
>>>
>>>   Justin A. Lemkul
>>>   Ph.D. Candidate
>>>   ICTAS Doctoral Scholar
>>>   MILES-IGERT Trainee
>>>   Department of Biochemistry
>>>   Virginia Tech
>>>   Blacksburg, VA
>>>   jalemkul[at]vt.edu   | (540)
>>>231-9080 
>>> 
>>>
>>>   http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin
>>> 
>>> >
>>> 

Re: [gmx-users] REMD problem

[Mark Abraham]

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 x 30   31   32   33 x 34   35   36   37 x 38   39   
40   41 x 42   43 x 44   45 x 46   47   48   49
Repl pr1.0   1.0   1.0   .00   1.0   
1.0   .00   1.0   1.0   1.0   1.0   .00   
1.0   .00   1.0   .00   1.0   .00   .46   
.00   1.0   .78   1.0   .00


Replica exchange at step 5750 time 11.5
Repl 0 <-> 1  dE = -7.583e+00
Repl ex  0 x  1234 x  56 x  78 x  9   10 x 11   
12 x 13   14 x 15   16 x 17   18 x 19   20   21   22   23   24 x 25   
26   27   28 x 29   30   31   32 x 33   34   35   36   37   38   39   
40 x 41   42 x 43   44   45   46   47   48   49
Repl pr   1.0   .00   1.0   1.0   1.0   1.0   
1.0   1.0   1.0   1.0   .48   .11   1.0   
.00   1.0   .00   1.0   .00   .00   .01   
1.0   1.0   .00   .01   .01


   Step   Time Lambda
   5800   11.60.0

   Energies (kJ/mol)
  AngleProper Dih.  Improper Dih.  LJ-14 
Coulomb-14
9.69806e+021.32207e+033.34938e+014.93171e+02   
-3.9e+03
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position 
Rest.
3.14374e+04   -6.42258e+02   -1.88529e+05   -2.01604e+04
0.0e+00
  PotentialKinetic En.   Total Energy  Conserved En.
Temperature
   -1.78987e+054.57462e+04   -1.33240e+051.23302e+10
5.62201e+02

 Pres. DC (bar) Pressure (bar)   Constr. rmsd
   -2.12803e+02   -5.47109e+022.21484e-05
...



Perhaps someone else can offer an explanation.  It should not be 
possible to run multiple replicas on a single processor.  Also note 
that your exchange probability is extremely high; you're likely not 
obtaining meaningful sampling.


If the MPI configuration allows physical processors to be 
over-allocated, then GROMACS is none the wiser.


Mark



-Justin

On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul > wrote:




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 cannot
think of a reason why 50 simulations could possibly run on 2 
processors.


-Justin

On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   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 are actually running, or at the 
very least

   you will get horribly slow performance.


   By the way, would you please show me where I can find the
   reasonable replex number information in the literature?
 I did
   not find it in the link you posted and the manual either.


   A few minutes of real literature searching will be far more
valuable
   than some random person on the Internet giving you a value
that you
   blindly use ;)

   -Justin

   Thanks.


   -- Best,
   Liang Liu


   -- ====

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu   | (540)
231-9080 


   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

>

   ====
   -- gmx-users mailing listgmx-users@gromacs.org

>

   http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] REMD problem

[Justin A. Lemkul]

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   39   40   41 x 
42   43 x 44   45 x 46   47   48   49
Repl pr1.0   1.0   1.0   .00   1.0   1.0 
  .00   1.0   1.0   1.0   1.0   .00   1.0   
.00   1.0   .00   1.0   .00   .46   .00   
1.0   .78   1.0   .00


Replica exchange at step 5750 time 11.5
Repl 0 <-> 1  dE = -7.583e+00
Repl ex  0 x  1234 x  56 x  78 x  9   10 x 11   12 x 
13   14 x 15   16 x 17   18 x 19   20   21   22   23   24 x 25   26   27 
  28 x 29   30   31   32 x 33   34   35   36   37   38   39   40 x 41   
42 x 43   44   45   46   47   48   49
Repl pr   1.0   .00   1.0   1.0   1.0   1.0   
1.0   1.0   1.0   1.0   .48   .11   1.0   
.00   1.0   .00   1.0   .00   .00   .01   
1.0   1.0   .00   .01   .01


   Step   Time Lambda
   5800   11.60.0

   Energies (kJ/mol)
  AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
9.69806e+021.32207e+033.34938e+014.93171e+02   -3.9e+03
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
3.14374e+04   -6.42258e+02   -1.88529e+05   -2.01604e+040.0e+00
  PotentialKinetic En.   Total Energy  Conserved En.Temperature
   -1.78987e+054.57462e+04   -1.33240e+051.23302e+105.62201e+02
 Pres. DC (bar) Pressure (bar)   Constr. rmsd
   -2.12803e+02   -5.47109e+022.21484e-05
...



Perhaps someone else can offer an explanation.  It should not be possible to run 
multiple replicas on a single processor.  Also note that your exchange 
probability is extremely high; you're likely not obtaining meaningful sampling.


-Justin

On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul > wrote:




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 cannot
think of a reason why 50 simulations could possibly run on 2 processors.

-Justin

On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   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 are actually running, or at the very least
   you will get horribly slow performance.


   By the way, would you please show me where I can find the
   reasonable replex number information in the literature?
 I did
   not find it in the link you posted and the manual either.


   A few minutes of real literature searching will be far more
valuable
   than some random person on the Internet giving you a value
that you
   blindly use ;)

   -Justin

   Thanks.


   -- Best,
   Liang Liu


   -- ====

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu   | (540)
231-9080 
   

   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

   >

   ====
   -- gmx-users mailing listgmx-users@gromacs.org

   >

   http://lists.gromacs.org/mailman/listinfo/gmx-users

   >
   Please search the archive at
   http://www.gromac

Re: [gmx-users] REMD problem

[Liu, Liang]

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
44   45 x 46   47   48   49
Repl pr1.0   1.0   1.0   .00   1.0   1.0
.00   1.0   1.0   1.0   1.0   .00   1.0   .00
1.0   .00   1.0   .00   .46   .00   1.0
.78   1.0   .00

Replica exchange at step 5750 time 11.5
Repl 0 <-> 1  dE = -7.583e+00
Repl ex  0 x  1234 x  56 x  78 x  9   10 x 11   12 x 13
  14 x 15   16 x 17   18 x 19   20   21   22   23   24 x 25   26   27   28 x
29   30   31   32 x 33   34   35   36   37   38   39   40 x 41   42 x 43
44   45   46   47   48   49
Repl pr   1.0   .00   1.0   1.0   1.0   1.0   1.0
1.0   1.0   1.0   .48   .11   1.0   .00
1.0   .00   1.0   .00   .00   .01   1.0   1.0
.00   .01   .01

   Step   Time Lambda
   5800   11.60.0

   Energies (kJ/mol)
  AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
9.69806e+021.32207e+033.34938e+014.93171e+02   -3.9e+03
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
3.14374e+04   -6.42258e+02   -1.88529e+05   -2.01604e+040.0e+00
  PotentialKinetic En.   Total Energy  Conserved En.Temperature
   -1.78987e+054.57462e+04   -1.33240e+051.23302e+105.62201e+02
 Pres. DC (bar) Pressure (bar)   Constr. rmsd
   -2.12803e+02   -5.47109e+022.21484e-05
...

On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul  wrote:

>
>
> 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 cannot think of a reason
> why 50 simulations could possibly run on 2 processors.
>
> -Justin
>
>  On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>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 are actually running, or at the very least
>>you will get horribly slow performance.
>>
>>
>>By the way, would you please show me where I can find the
>>reasonable replex number information in the literature?  I did
>>not find it in the link you posted and the manual either.
>>
>>
>>A few minutes of real literature searching will be far more valuable
>>than some random person on the Internet giving you a value that you
>>blindly use ;)
>>
>>-Justin
>>
>>Thanks.
>>
>>
>>-- Best,
>>Liang Liu
>>
>>
>>-- ==**__==
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin
>>
>> 
>> >
>>
>>==**__==
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>> 
>> >
>>Please search the archive at
>>
>> http://www.gromacs.org/__**Support/Mailing_Lists/Search
>>
>> >
>> before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>> >.
>>
>>Can't post? Read 
>> http://www.gromacs.org/__**Support/Mailing_Lists
>>
>> 
>> >
>>
>>
>>
>>
>> --
>> Best,
>> Liang Liu
>>
>
> --
> 

Re: [gmx-users] REMD problem

[Justin A. Lemkul]

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 cannot think of a reason why 50 
simulations could possibly run on 2 processors.


-Justin

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
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 are actually running, or at the very least
you will get horribly slow performance.


By the way, would you please show me where I can find the
reasonable replex number information in the literature?  I did
not find it in the link you posted and the manual either.


A few minutes of real literature searching will be far more valuable
than some random person on the Internet giving you a value that you
blindly use ;)

-Justin

Thanks.


-- 
Best,

Liang Liu


-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080

http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


==__==
-- 
gmx-users mailing listgmx-users@gromacs.org


http://lists.gromacs.org/__mailman/listinfo/gmx-users

Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
 before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists





--
Best,
Liang Liu


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] REMD problem

[Liu, Liang]

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 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 are actually running, or at the very least you will get horribly
> slow performance.
>
>
>  By the way, would you please show me where I can find the reasonable
>> replex number information in the literature?  I did not find it in the link
>> you posted and the manual either.
>>
>>
> A few minutes of real literature searching will be far more valuable than
> some random person on the Internet giving you a value that you blindly use
> ;)
>
> -Justin
>
>  Thanks.
>>
>>
>> --
>> Best,
>> Liang Liu
>>
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Best,
Liang Liu
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] REMD problem

[Justin A. Lemkul]

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 are actually running, or at the very least you will get horribly slow 
performance.


By the way, would you please show me where I can find the reasonable 
replex number information in the literature?  I did not find it in the 
link you posted and the manual either.




A few minutes of real literature searching will be far more valuable than some 
random person on the Internet giving you a value that you blindly use ;)


-Justin


Thanks.


--
Best,
Liang Liu


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] REMD problem

[Liu, Liang]

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 did not find it in the link you
posted and the manual either.

Thanks.


-- 
Best,
Liang Liu
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] REMD problem

[Justin A. Lemkul]

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.  If you want 50 replicas, you need at least 50 processors, 
ideally more.



How to choose a reasonable number for -replex? the smaller the better?



Please consult the literature.

-Justin


Thanks again.

On Wed, Sep 28, 2011 at 3:06 PM, Justin A. Lemkul > wrote:




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 numbers for np, multi or replex?


Current Gromacs versions allow more than one processor per REMD
simulation. Please refer to the link I provided before for
specifics.  You need all of the replicas to run at roughly the same
speed so the number of processors per simulation should be the same.


Is the simulation time still set in the mdp file with nsteps and
dt? e.g. nsteps = 50 and dt = 0.002 to run a 1ns simulation?


It's just like any other simulation in this regard.

-Justin

Any helps will be highly appreciated.

On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   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)". What is this for?


   You have to run mdrun_mpi as a process under mpirun, e.g.:

   mpirun -np 10 mdrun_mpi -s md.tpr (etc)

   -Justin

   On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

>
   
>>
  
>
   
 wrote:



 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 shows as "Need at
least two
  replicas for
 replica exchange (option -multi)", what is this
   for? Thanks.



 You have to use the -multi flag.  Otherwise all
mdrun
   does is run
 md.tpr and try to do REMD with nothing.

 
 http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps



 
 >
   
 

Re: [gmx-users] REMD problem

[Liu, Liang]

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.
>>
>> 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 replex?
>>
>>
> Current Gromacs versions allow more than one processor per REMD simulation.
> Please refer to the link I provided before for specifics.  You need all of
> the replicas to run at roughly the same speed so the number of processors
> per simulation should be the same.
>
>
>  Is the simulation time still set in the mdp file with nsteps and dt? e.g.
>> nsteps = 50 and dt = 0.002 to run a 1ns simulation?
>>
>>
> It's just like any other simulation in this regard.
>
> -Justin
>
>  Any helps will be highly appreciated.
>>
>> On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>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)". What is this for?
>>
>>
>>You have to run mdrun_mpi as a process under mpirun, e.g.:
>>
>>mpirun -np 10 mdrun_mpi -s md.tpr (etc)
>>
>>-Justin
>>
>>On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   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 A. Lemkul
>>   mailto:jalem...@vt.edu>
>>>
>>   
>>>
>>
>>
>>  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 shows as "Need at least two
>>   replicas for
>>  replica exchange (option -multi)", what is this
>>for? Thanks.
>>
>>
>>
>>  You have to use the -multi flag.  Otherwise all mdrun
>>does is run
>>  md.tpr and try to do REMD with nothing.
>>
>>http://www.gromacs.org/__**
>> Documentation/How-tos/REMD#___**___Execution_Steps
>>> _Execution_Steps
>> >
>>  > Documentation/How-tos/REMD#___**_Execution_Steps
>>> Execution_Steps
>> >>
>>> Documentation/How-tos/REMD#___**_Execution_Steps
>>> Execution_Steps
>> >
>>  > Documentation/How-tos/REMD#__**Execution_Steps
>>> Execution_Steps
>> >>>
>>
>>  -Justin
>>
>>  -- ==**__==
>>
>>  Justin A. Lemkul

Re: [gmx-users] REMD problem

[Justin A. Lemkul]

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 numbers for np, multi or replex?



Current Gromacs versions allow more than one processor per REMD simulation. 
Please refer to the link I provided before for specifics.  You need all of the 
replicas to run at roughly the same speed so the number of processors per 
simulation should be the same.


Is the simulation time still set in the mdp file with nsteps and dt? 
e.g. nsteps = 50 and dt = 0.002 to run a 1ns simulation?




It's just like any other simulation in this regard.

-Justin


Any helps will be highly appreciated.

On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul > wrote:




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)". What is this for?


You have to run mdrun_mpi as a process under mpirun, e.g.:

mpirun -np 10 mdrun_mpi -s md.tpr (etc)

-Justin

On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   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 A. Lemkul
   mailto:jalem...@vt.edu>
>
   

 
 >
   
 
 
 >>

  -Justin

  -- ==__==

  Justin A. Lemkul
  Ph.D. Candidate
  ICTAS Doctoral Scholar
  MILES-IGERT Trainee
  Department of Biochemistry
  Virginia Tech
  Blacksburg, VA
  jalemkul[at]vt.edu  
 | (540)

   231-9080 
  

 
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


   >

 

 
 >>

  ==__==
  -- gmx-users mailing listgmx-users@gromacs.org

   

Re: [gmx-users] REMD problem

[Liu, Liang]

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 replex?

Is the simulation time still set in the mdp file with nsteps and dt? e.g.
nsteps = 50 and dt = 0.002 to run a 1ns simulation?

Any helps will be highly appreciated.

On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul  wrote:

>
>
> 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)". What is this for?
>>
>>
> You have to run mdrun_mpi as a process under mpirun, e.g.:
>
> mpirun -np 10 mdrun_mpi -s md.tpr (etc)
>
> -Justin
>
>  On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>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 A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   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 shows as "Need at least two
>>replicas for
>>   replica exchange (option -multi)", what is this for? Thanks.
>>
>>
>>
>>   You have to use the -multi flag.  Otherwise all mdrun does is
>> run
>>   md.tpr and try to do REMD with nothing.
>>
>>  http://www.gromacs.org/**
>> Documentation/How-tos/REMD#___**_Execution_Steps
>>> Execution_Steps
>> >
>>  > Documentation/How-tos/REMD#__**Execution_Steps
>>> Execution_Steps
>> >>
>>
>>   -Justin
>>
>>   -- ==**==
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   MILES-IGERT Trainee
>>   Department of Biochemistry
>>   Virginia Tech
>>   Blacksburg, VA
>>   jalemkul[at]vt.edu   | (540)
>>
>>231-9080 
>>   
>>
>>   http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin
>>
>> 
>> >
>>
>>   >
>> 
>> >>
>>
>>   ==**==
>>   -- gmx-users mailing listgmx-users@gromacs.org
>>
>>   **>
>>
>>
>>   
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>>
>> 
>> >
>>   
>> 
>>
>> 
>> >>
>>   Please search the archive at
>>   
>> http://www.gromacs.org/**Support/Mailing_Lists/Search
>>
>> 
>> >
>>   
>> 
>>

Re: [gmx-users] REMD problem

[Justin A. Lemkul]

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)". What is this for?




You have to run mdrun_mpi as a process under mpirun, e.g.:

mpirun -np 10 mdrun_mpi -s md.tpr (etc)

-Justin

On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul > wrote:




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 A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   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 shows as "Need at least two
replicas for
   replica exchange (option -multi)", what is this for? Thanks.



   You have to use the -multi flag.  Otherwise all mdrun does is run
   md.tpr and try to do REMD with nothing.

 
 http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps


 
 >

   -Justin

   -- ====

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu   | (540)
231-9080 
   

   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

   >

   ====
   -- gmx-users mailing listgmx-users@gromacs.org

   >

   http://lists.gromacs.org/mailman/listinfo/gmx-users

   >
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-- 
Best,

Liang Liu


-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080

http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


==__==
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Re: [gmx-users] REMD problem

[Liu, Liang]

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, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul  wrote:

>
>
> 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 A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>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 shows as "Need at least two replicas for
>>replica exchange (option -multi)", what is this for? Thanks.
>>
>>
>>
>>You have to use the -multi flag.  Otherwise all mdrun does is run
>>md.tpr and try to do REMD with nothing.
>>
>>http://www.gromacs.org/__**Documentation/How-tos/REMD#__**
>> Execution_Steps
>>
>> 
>> >
>>
>>-Justin
>>
>>-- ==**__==
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin
>>
>> 
>> >
>>
>>==**__==
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>> 
>> >
>>Please search the archive at
>>
>> http://www.gromacs.org/__**Support/Mailing_Lists/Search
>>
>> >
>> before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>> >.
>>
>>Can't post? Read 
>> http://www.gromacs.org/__**Support/Mailing_Lists
>>
>> 
>> >
>>
>>
>>
>>
>> --
>> Best,
>> Liang Liu
>>
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Best,
Liang Liu
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] REMD problem

[Justin A. Lemkul]

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 A. Lemkul > wrote:




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 shows as "Need at least two replicas for
replica exchange (option -multi)", what is this for? Thanks.



You have to use the -multi flag.  Otherwise all mdrun does is run
md.tpr and try to do REMD with nothing.

http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps


-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080

http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


==__==
-- 
gmx-users mailing listgmx-users@gromacs.org


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.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists





--
Best,
Liang Liu


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] REMD problem

[Liu, Liang]

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,
>> 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 two replicas for replica
>> exchange (option -multi)", what is this for? Thanks.
>>
>>
>>
> You have to use the -multi flag.  Otherwise all mdrun does is run md.tpr
> and try to do REMD with nothing.
>
> http://www.gromacs.org/**Documentation/How-tos/REMD#**Execution_Steps
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Best,
Liang Liu
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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