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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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
-- 
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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
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>



-- 
Best,
Liang Liu
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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

   >

   ====
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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
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>>> >.
>>
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>> 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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Liang Liu
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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


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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]

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
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Re: [gmx-users] REMD problem

[Justin A. Lemkul]

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


--
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RE: [gmx-users] REMD problem in concept

[Berk Hess]

Hi,

I think you are talking about two different concepts.
At the moment of switching the replicas, the potential energy
does not change, because the force field is temperature indepent.
This is what Chris meant.
As the system evolves in time, the potential energy will go up
when a replica is switched to a higher temperature.

Berk

> Date: Thu, 4 Dec 2008 03:19:17 +1100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] REMD problem in concept
> 
> [EMAIL PROTECTED] wrote:
> > dG=dH-TdS
> > 
> > so as T increases, so does the entropic contribution to the free energy 
> > (=available energy). The potential energies stay the same when using a 
> > temperature-independent forcefield (like all of the ones that come with 
> > gromacs).
> 
> That's not quite right. The average total energy (H, above) increases 
> with T, and the equipartition theorem requires that for a typical MD 
> system in thermal equilibrium, some of that energy must go to increased 
> average PE. The form of the forcefield doesn't change, of course. This 
> KE-PE-TE behaviour can be readily observed in an REMD simulation and is 
> documented in various graphs in various REMD papers.
> 
> > Your system will easily cross barriers on the order of KbT and thus 
> > barriers are more easily crossed at higher temperature.
>  >
> > Nearly every RE paper has an introductory section that goes over these 
> > topics in more or less detail. I suggest that you read the introduction 
> > and theory sections of about 10 of them and you should by then 
> > understand it very well.
> 
> Yep, agreed.
> 
> Mark
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Re: [gmx-users] REMD problem in concept

[Mark Abraham]

[EMAIL PROTECTED] wrote:

dG=dH-TdS

so as T increases, so does the entropic contribution to the free energy 
(=available energy). The potential energies stay the same when using a 
temperature-independent forcefield (like all of the ones that come with 
gromacs).


That's not quite right. The average total energy (H, above) increases 
with T, and the equipartition theorem requires that for a typical MD 
system in thermal equilibrium, some of that energy must go to increased 
average PE. The form of the forcefield doesn't change, of course. This 
KE-PE-TE behaviour can be readily observed in an REMD simulation and is 
documented in various graphs in various REMD papers.


Your system will easily cross barriers on the order of KbT and thus 
barriers are more easily crossed at higher temperature.

>
Nearly every RE paper has an introductory section that goes over these 
topics in more or less detail. I suggest that you read the introduction 
and theory sections of about 10 of them and you should by then 
understand it very well.


Yep, agreed.

Mark
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Re: [gmx-users] REMD problem in concept

[Mark Abraham]

sarbani chattopadhyay wrote:

  Hi,
Thank you for the reply. But in that case what helps the replica at 
higher temperature cross the energy barrier? At higher temperature the 
velocities will be higher.


For the same reason it can cross more easily at high T in non-REMD: when 
there is more KE going around, PE barriers are less significant. The 
nature of the free-energy surface can also be temperature dependent.


Mark
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Re: Re: [gmx-users] REMD problem in concept

[sarbani chattopadhyay]

  Hi,
 Thank you for the reply. But in that case what helps the replica at higher 
temperature cross the energy barrier? At higher temperature the velocities will 
be higher.

Thanks in advance,
Sarbani


On Tue, 02 Dec 2008 Mark Abraham wrote :
>sarbani chattopadhyay wrote:
>>   Hi everybody,
>>   I am having a doubt whether I have understood the 
>> concepts of Replica
>>exchange molecular dynamics correctly or not.
>>   When a pair of replicas are exchanged, the one at 
>> higher temperature thet has
>>higher velocities, (which are rescaled after the exchange) comes with a 
>>higher energy. It's
>>kinetic energy gets reduced as velocities are rescaled. Thus its potential 
>>energy increases.
>
>Kinetic energy is a function of the velocities, potential energy is a function 
>of the positions. So velocity rescaling will not have any instantaneous effect 
>on the PE.
>
>>What happens to the replica that was at lower temperature? It's velocities 
>>need to be increased
>>to maintain the temperature. What happens to it's potential energy then?
>
>As before, nothing.
>
>>I may be missing a very basic point and any suggestion regarding this will be 
>>highly helpful.
>
>Once the simulation continues, things are still normal. The reason the 
>exchange occurred was that the positions were such that the PE was close 
>enough that detailed balance for the generalized ensemble was preserved  
>during the swap. Thus the ensembles before and after the exchange are also 
>still well-formed.
>
>Mark
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Re: [gmx-users] REMD problem in concept

[Mark Abraham]

sarbani chattopadhyay wrote:

  Hi everybody,
  I am having a doubt whether I have understood the 
concepts of Replica

exchange molecular dynamics correctly or not.
  When a pair of replicas are exchanged, the one at 
higher temperature thet has
higher velocities, (which are rescaled after the exchange) comes with a 
higher energy. It's
kinetic energy gets reduced as velocities are rescaled. Thus its 
potential energy increases.


Kinetic energy is a function of the velocities, potential energy is a 
function of the positions. So velocity rescaling will not have any 
instantaneous effect on the PE.


What happens to the replica that was at lower temperature? It's 
velocities need to be increased

to maintain the temperature. What happens to it's potential energy then?


As before, nothing.

I may be missing a very basic point and any suggestion regarding this 
will be highly helpful.


Once the simulation continues, things are still normal. The reason the 
exchange occurred was that the positions were such that the PE was close 
enough that detailed balance for the generalized ensemble was preserved 
 during the swap. Thus the ensembles before and after the exchange are 
also still well-formed.


Mark
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