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Lecture 14 notes
#9435 01/23/06 07:39 PM
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Lecture 14
Section one: Replica Exchange Molecular Dynamics (lecture notes attached), by Richard M. Venable

Section two: Images and the use of symmetry, by Bernard R. Brooks

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Xiongwu Wu, Ph.D
NIH, NHLBI
5635 Fishers Lane, Room T904, MSC 9314
Bethesda, MD 20892-9314
Re: Lecture 14 notes
wxw #9436 02/02/06 10:19 PM
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An added note on the ad hoc REX package in the Lecture 14 notes; I have put together an improved version of this package, which fixes a few minor issues, and generally reduces the amount of file editing required.

Please contact me for the NEW! IMPROVED! package, rather than attempting to use the script and progs found in the lecture notes.

Regards,


Rick Venable
computational chemist

modified ad hoc replica exchange package
rmv #9437 09/29/06 02:59 AM
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I've translated the the C and Python code into a single Fortran program, with the swap step range, cleanup frequency, number of T baths, and the T values all read from a simple config file. The .csh scripts were re-written to use the config file as well. The program should only need to be compiled once for a particular computer system. Anyone interested in this greatly improved package should contact me via email.


Rick Venable
computational chemist

Re: modified ad hoc replica exchange package *DELETED*
rmv #9438 10/28/06 05:00 PM
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Rick Venable
computational chemist

BUGFIX for modified ad hoc replica exchange package
rmv #9439 11/14/06 11:42 PM
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Attached is a modified package which fixes a major bug not found in my initial tests (a user found it and reported to me). The symptom is seen in the log file as an energy of 0.00 for one of the configs, and a swap probability of INF (infinity). There are 2 changes for this, one in the Trex.f program, the other in the rexstart.inp and rex.inp CHARMM scripts. Other than recompiling the program, the other change for users is the following addition (in red) to the input scripts--

! KEEP THIS NEXT BIT
open unit 12 write card name @TACT/rex.ene
format (F20.6)
write title unit 12
* ?ENER
*


With this change, the energy values are transmitted between programs w/o errors (at least in all my tests so far).

I made a few other minor changes, esp. for the log file, which is now named based on the last swap step it will perform. The frxn-swap.csh script was also changed to reflect the log file name change.

Attached Files
12274-adhoctrex.tar.gz (0 Bytes, 904 downloads)

Rick Venable
computational chemist

Re: BUGFIX for modified ad hoc replica exchange package
rmv #9440 11/18/06 04:48 PM
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Please check this thread for new info and updated packages; I am currently investigating changes to support the use of the NPT ensemble. For informational purpose, the latest AdHocTrex package README.txt follows:

The TREX ad hoc interface to CHARMM for REMD
November 2006 Update

---------------------------------------------------------------------
N.B.: The initial release had a bug in passing energy values,
and incorrect swaps could occur; this release fixes that bug and a
couple other minor issues. The bug symptom is an infinite probability
(seen as INF with g77), and an energy of 0.00 for one of the baths.
---------------------------------------------------------------------

An interface to CHARMM for temperature based replica exchange is
described, using a custom Fortran program, and taking advantage of the
dynamics restart capabilities. Some editing of the scripts is needed
as part of the setup; however, the interface is fairly flexible for this
same reason. The programs and scripts are presented in the form used to
perform some test REMD simulations on gel phase bilayers of the lipid
DMPC (40 T baths, 250 MD steps, 4000 swaps; 1 ns), and a single lipid
test (10 baths, more widely spaced; 2 ns).
This is an original translation of the C and Python code from
the authors of "Optimal estimates of free energies from multi-state
nonequilibrium work data", Paul Maragakis, Martin Spichty, and Martin
Karplus, PHYS REV LETT 96 (10): Art. No. 100602 MAR 17 2006.

The Fortran program controls the synchronization of the MD
simulations and swaps, and calls various other programs (including CHARMM).
After each MD run, the final potential energy is used to evaluate the
Metropolis criterion; for a swap, the CHARMM restart files are exchanged,
and the velocities are scaled based on the T change. From dynamc.doc, the
feature used to scale the velocities is:

----------------------------------------------------------------
ISCALE 0 This option is to allow the user to scale the velocities
by a factor SCALE at the beginning of a restart run.
This may be useful in changing the desired temperature.
.eq. 0 no scaling done (usual input value)
.ne. 0 scale velocities by SCALE.
WARNING: Please use this option only when you are changing the
temperature of the run.
SCALE 1. Scale factor for the previous option.
----------------------------------------------------------------

The value of SCALE is 1.0 unless a swap occurs; for a swap, the value
computed from the square root of the T ratio is used. The values are
communicated to CHARMM by a formatted file, which is read via the STREAM
command. The final energy (?ENER) from each MD run is written to a file
using the WRITE TITLE feature.

REMD is embarassingly parallel; it is ideally suited to Linux
clusters, as there is no communication between processes except via
files between the short MD runs, and each process is self contained.
Parallel MD, on the other hand, must exchange a fair amount of data
between all processes on every integration step, esp. if particle-mesh
Ewald (PME) summation is being used. It's simplest to use one processor
for each T bath, although it is certainly possible and reasonable (but
more complicated) to use both processors in a dual-processor compute
node. However, for a fixed number of nodes, it may often be better to
have twice as many T baths than to double the speed.

In order to help manage the output, a cleanup script is called
every N swap steps from the Trex program, performing: [1] deletion of
unneeded restart files, [2] gzip compression and relocation of output
files, and [3] merge of the trajectories into larger files and deletion
of the originals (via merge.inp). Without these steps, one can easily
become overwhelmed by the number of files produced and the disk space used.

The following listing outlines the steps required to use this
collection of scripts and programs to perform REMD with CHARMM:

* compile Trex.f via e.g.

% set path = ( /usr/local/mpich-gnu/bin $path )
% mpif77 Trex.f -o Trex.ix

On a given cluster, the program should only need to be compiled
once in a while, for new machine types or possibly software updates. The
remaining steps apply to each REMD simulation.
* Choose the number of T baths and the spacing between baths; some
iterative tests may be needed to get the optimum spacing and to maximize
the T range for a fixed number of baths; integer T values are assumed
* Decide how many MD steps to perform between swaps, and how many swap
steps for a particular run; again, some initial tests may be needed.
* Based on these choices, create the config file (see below)
* Create a link named "charmm" in the working directory that points to
a single threaded (non-parallel) version of CHARMM; on NIH Biowulf use
something like

% ln -s /usr/local/charmm/c31b2/pgi-med.one charmm

* Edit rexstart.inp, rex.inp, and init.str based on the number of MD
steps and protocol, and the actual files (RTF, PARAM, PSF, COOR, etc.)
that will be used; note that at least one coord set must be written to
the .trj file.
* Edit the merge.inp script, to set the SKIP interval for MERGE
* Edit the run_rex.csh script if needed, e.g. for some other queuing
system besides PBS, or for the location of the MPICH installation.
* Run the rex_init.csh script; it sets up the subdirs for each T
bath, and requires the config filename as an argument
* Submit (PBS) the run_rex.csh script to start the replica exchange;
the example passes 2 args, the number of baths and the config filename

Monitoring the swap acceptance

Also included are a couple means of monitoring the swaps and the
acceptance rate:

* frxn-swap.csh; computes the overall acceptance, and that for each bath
from data in the rexswapN.log files; config file arg, prints a table
* smove-temp.py; a Python program, which must be edited (T bath list)
prior to use; this produces data suitable for the 'xmgrace' program via

% smove-temp.py > aswap.dat
% xmgrace aswap.dat


Restart; extending a run, or after a failure

Continuation after a successful completion is straightforward;
simply change the first and last swap step in the config file, as
indicated in the detailed description of the config file below. Then
submit the run_rex.csh script to the PBS queue as before.
If a run stops early because of a node failure, network
disruption, or some other problem, it can also be continued, but a
couple of additional steps are needed. The steps are:

[1] determine the last two file numbers, which should represent the
swap step MD in progress, and the last completed swap step; I use

% ls -str 293

[2] verify the status for all baths; if the last 2 file numbers are
e.g. 694 and 695, the command

% ls -s ???/rex.trj.69[45]

will produce a listing of the last two .trj files for all baths, and
their size (in blocks); for the running step which failed, one or more
of the rex.trj.695 files will have a zero size

[3] in order to preserve the log data, change the name of the log file
to reflect the last completed step, e.g.

% mv rexswap4000.log rexswap694.log

[4] edit the config file, and change the first step number to that of
the step that failed in progress (695 for this example)

[5] resubmit run_rex.csh to a PBS batch queue


Additional notes on CHARMM input scripts

The filenames rexstart.inp and rex.inp should probably be
preserved in order to avoid breaking the package; however, there is
a great deal of latitude for the contents of the setup (init.str) and
the short dynamics run (rex*inp) scripts. The example subdirs indicate
a couple choices, vacuum sampling and condensed phase sampling; the
latter is more difficult and requires a fairly close T bath spacing.
They may not be ideal examples and are not test cases, but are meant
to illustrate the usage of the package. The number of dynamics steps
and the T bath choices may not be ideal; I'm still expolring these
issues myself.
The merge.inp script currently prunes the trajectory files to
1 ps intervals for the lowest T bath, and to 5 ps intervals for all other
baths. Other than changing the SKIP value for saving coord sets, this
file should not require any further editing. The example1 subdir has
another script which further merges the files to 1 ns sizes, in order to
faciliate analysis of the results.

Configuration file format

My convention has been to use .cfg as the extension for the
config file, but any extension may be used. The first 4 lines of the file
specify key parameters; the remaining lines are the integer values for the
T baths. For the first 4 lines, the first 5 chars of each is a label;
the integer values should start in col 6 or 7. The data is read based on
order; the first line should be the number of the first swap step for this
particular run, etc. A simple example:

FIRST 1
LAST 4000
CLEAN 80
NBATH 5
300
330
370
420
480

The labels indicate:

FIRST the first swap step; 1 to start, e.g. 4001 to continue
LAST the last swap step; 1+(LAST-FIRST) CHARMM runs of rex*.inp
CLEAN frequency for running cleantemp.csh; must be < 90
NBATH the number of T bath values on the following lines

Note that rextart.inp is only run for the very first swap step, i.e.
step 1 when FIRST is 1. To continue the above run, the config file
would be changed as indicated below, and run_rex.csh re-submitted to
the PBS queue.

FIRST 4001
LAST 8000
CLEAN 80
NBATH 5
300
330
370
420
480


File manifest

Trex.f master Fortran prog

rex_init.csh set up the T bath subdirs
run_rex.csh script to submit to PBS queue for REX
cleantemp.csh periodically called to cleanup
rexdone.csh optional cleanup after completion
frxn-swap.csh monitor swap acceptance
smove-temp.py build data for moves plot (xmgrace)

example1 subdir illustrating vacuum sampling of a lipid
dppc10.cfg sample config file; 10 T baths
init.str CHARMM initialization; read some files
rexstart.inp the first MD run; write .res and .ene files
rex.inp all other MD runs; reads .res
merge.inp merges .trj files (cleantemp.csh)
postmerg.inp secondary merge to 1 ns chunks for analysis

example2 subdir illustrating condensed phase sampling
dmpc40.cfg sample config file; 40 T baths
init.str CHARMM initialization; read some files
rexstart.inp the first MD run; write .res and .ene files
rex.inp all other MD runs; reads .res
merge.inp merges .trj files (cleantemp.csh)

README.txt this description
Bibliography.txt 2004-2005 publications using replica exchange


Rick Venable
computational chemist

NPT modified ad hoc replica exchange package
rmv #9441 05/29/08 01:48 AM
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The long promised NPT version is attached to this message.

Attached Files
18170-nptrex.tar.gz (0 Bytes, 708 downloads)

Rick Venable
computational chemist


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