AMBER Archive (2005)

Subject: Re: AMBER: Replica-Exchange MD from AMBER8!

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Sat Dec 03 2005 - 15:11:07 CST

after the initial MD setup (the rem.out with no #), the
inpcrd name is switched to the restart. that way the restart
of 1 MD run is used for the input for the next run after
the exchange attempt. so, this means that your data is correct.

Peng Tao wrote:

> Dr. Carlos Simmerling,
>
> There is one more strange thing I just noted.
>
> In the command line to run sander, the initial coordinate of the
> system is given by inpcrd file, and restart file will be saved to
> restrt file.
>
> But something strange happened to my REMD run with two replicas.
>
> My two INPCRD files are md.r.000 and md.r.001 without temperature. But
> it seemed that these two INPCRD files have not been used for two REMD
> replicas.
>
> Here are what I got in sander output files.
>
> The head of pre-md run output file rem.out:
> ///////////////////////////////////////////////////////////////////
>
> -------------------------------------------------------
> Amber 8 SANDER Scripps/UCSF 2004
> -------------------------------------------------------
>
> | Run on 12/03/2005 at 15:00:48
> [-O]verwriting output
>
> File Assignments:
> | MDIN:
> rem.in.000
> | MDOUT:
> rem.out
> |INPCRD:
> md.r.000
> | PARM:
> prmtop
> |RESTRT:
> rem.rstrt.000
> | REFC:
> refc
> | MDVEL:
> mdvel
> | MDEN:
> mden.000
> | MDCRD:
> rem.traj
> |MDINFO:
> rem.mdinfo
> |INPDIP:
> inpdip
> |RSTDIP:
> rstdip
>
>
> Here is the input file:
>
> md9.in <http://md9.in> - PyrFurDuplex gb test run, igb =
> 1
> &cntrl
>
> imin = 0, nstlim = 5000, dt =
> 0.002,
> ntx = 5, tempi = 0.0, temp0 =
> 267.0,
> ntt = 1, tol = 0.000001, saltcon =
> 0.2,
> ntc = 2, ntf = 1, ntb = 0, nsnb =
> 20,
> ntwx = 10, ntwe = 0, ntwr = 500, ntpr =
> 500,
> scee = 1.2, cut =
> 99.0,
> ntr = 0, tautp = 0.1, offset =
> 0.09,
> nscm = 500, igb = 1, numexchg =
> 2,
> irest = 1, ntave =
> 0,
> /
>
> ///////////////////////////////////////////////////////////////////
>
> In this run, md.r.000 has been used as INPCRD file. And rem.rstrt.000
> is output file.
>
>
>
> In one replica run, the output file rem.out.000 has head
>
> //////////////////////////////////////////////////////////////////
>
> -------------------------------------------------------
> Amber 8 SANDER Scripps/UCSF 2004
> -------------------------------------------------------
>
> | Run on 12/03/2005 at 15:01:43
> [-O]verwriting output
>
> File Assignments:
> | MDIN:
> rem.in.000
> | MDOUT:
> rem.out.000
> |INPCRD:
> rem.rstrt.000
> | PARM:
> prmtop
> |RESTRT:
> rem.rstrt.000
> | REFC:
> refc
> | MDVEL:
> mdvel
> | MDEN:
> mden.000
> | MDCRD:
> rem.traj.000
> |MDINFO:
> rem.mdinfo.000
> |INPDIP:
> inpdip
> |RSTDIP:
> rstdip
>
>
> Here is the input file:
>
> md9.in <http://md9.in> - PyrFurDuplex gb test run, igb =
> 1
> &cntrl
>
> imin = 0, nstlim = 5000, dt =
> 0.002,
> ntx = 5, tempi = 0.0, temp0 =
> 267.0,
> ntt = 1, tol = 0.000001, saltcon =
> 0.2,
> ntc = 2, ntf = 1, ntb = 0, nsnb =
> 20,
> ntwx = 10, ntwe = 0, ntwr = 500, ntpr =
> 500,
> scee = 1.2, cut =
> 99.0,
> ntr = 0, tautp = 0.1, offset =
> 0.09,
> nscm = 500, igb = 1, numexchg =
> 2,
> irest = 1, ntave =
> 0,
> /
>
>
> ///////////////////////////////////////////////////////////////////
>
> In this run, rem.rstrt.000 is INPCRD file, and again, rem.rstrt.000 is
> also RESTRT file. I am confused by this, because I thought md.r.000 is
> suposed to be INPCRD for this run.
>
>
>
> In another run, output file rem.out.001 has head as
>
> ///////////////////////////////////////////////////////////////////
>
> -------------------------------------------------------
> Amber 8 SANDER Scripps/UCSF 2004
> -------------------------------------------------------
>
> | Run on 12/03/2005 at 15:01:43
> [-O]verwriting output
>
> File Assignments:
> | MDIN:
> rem.in.001
> | MDOUT:
> rem.out.001
> |INPCRD:
> rem.rstrt.001
> | PARM:
> prmtop
> |RESTRT:
> rem.rstrt.001
> | REFC:
> refc
> | MDVEL:
> mdvel
> | MDEN:
> mden.001
> | MDCRD:
> rem.traj.001
> |MDINFO:
> rem.mdinfo.001
> |INPDIP:
> inpdip
> |RSTDIP:
> rstdip
>
>
> Here is the input file:
>
> md9.in <http://md9.in> - PyrFurDuplex gb test run, igb =
> 1
> &cntrl
>
> imin = 0, nstlim = 5000, dt =
> 0.002,
> ntx = 5, tempi = 0.0, temp0 =
> 289.0,
> ntt = 1, tol = 0.000001, saltcon =
> 0.2,
> ntc = 2, ntf = 1, ntb = 0, nsnb =
> 20,
> ntwx = 10, ntwe = 0, ntwr = 500, ntpr =
> 500,
> scee = 1.2, cut =
> 99.0,
> ntr = 0, tautp = 0.1, offset =
> 0.09,
> nscm = 500, igb = 1, numexchg =
> 2,
> irest = 1, ntave =
> 0,
> /
>
>
> ///////////////////////////////////////////////////////////////////
>
> Again, rem.rstrt.001 is both INPCRD and RESTRT file. The other INPCRD
> file md.r.001 seemed not be used at all in the REMD simulation.
>
> Did I messed up some input files again?
>
> The PBS setup file:
>
> ///////////////////////////////////////////////////////////////////
>
> #PBS -N olig8HelRGBREMDtest.in
> #PBS -l mem=50mw
> #PBS -l walltime=533
> #PBS -l nodes=2:ppn=1
> #PBS -j oe
> #PBS -m ae
> #PBS -S /bin/csh
>
>
> module load amber
> setenv AMBERHOME /usr/local/amber/amber8
>
> set
> WORKDIR=/a/osu3112/work/crc/project1/oligomer/gbmd/oligomer8/helixR/run05REMDtest
>
> #cd
> /a/osu3112/work/crc/project1/oligomer/gbmd/oligomer8/helixR/run05REMDtest
>
> #cd $TMPDIR
>
> #cp $WORKDIR/* .
>
> cd $WORKDIR
>
>
> set MDIN=rem.in <http://rem.in>
> set MDOUT=rem.out
> set MDEN=rem.mden
> set MDVEL=rem.mevel
> set MDINFO=rem.mdinfo
> set PRMTOP=prmtop
> set INPCRD=md.r
> set TRAJ=rem.traj
> set RESTRT=rem.rstrt
>
> mpiexec /usr/local/amber/amber8/exe/sander.REM -O -ng 2 -rem 1
> -remlog olig8HelRGBREMD.log -i $MDIN -o $MDOUT -inf $MDINFO -p
> $PRMTOP -x $TRAJ -c $INPCRD -r $RESTRT
>
> #cp * $WORKDIR
>
> ls -al
> pwd
>
> ///////////////////////////////////////////////////////////////////
>
> By the way, two restart file rem.restrt.000 and rem.restrt.001 weren't
> there at all.
>
> I also attached all the files except three large trajectory files.
>
> Thanks again for your help.
>
> Best regards,
> Peng Tao
>
>
>
> On 12/2/05, *Carlos Simmerling* <carlos.simmerling_at_stonybrook.edu
> <mailto:carlos.simmerling_at_stonybrook.edu>> wrote:
>
> I think that one problem is that both of your inpcrd files
> (rem.rstrt.00X) have
> a temperature of 300K in the header. In REMD, the temp0 values is
> placed in the restart file for reading in the next MD step. These will
> override any value in the mdin. So, delete the third number on the
> second line of
> the restarts and try again.
>
> amber9 will have bettter error checking of this sort of thing- but
> with
> amber8, if 2 replicas are at the same T it can cause problems with
> the exchange calculation.
>
> try this fix and let me know if it still behaves strangely.
> carlos
>
> Peng Tao wrote:
>
> > Dear all,
> >
> >
> > I am trying to use REMD from AMBER8, but I have some problem to use
> > this program.
> >
> > First I run the examples of REMD downloaded from AMBER home page
> > ( amber.scripps.edu <http://amber.scripps.edu>
> <http://amber.scripps.edu>)
> > Replica exchange (REM) test suite for Amber 8:
> > http://amber.scripps.edu/amber8.remtests.tar.gz
> <http://amber.scripps.edu/amber8.remtests.tar.gz>
> >
> > I used rem_gbrun example, because I am using GB model in my current
> > research.
> >
> > Fortunately, I can run this test successfully. That means, when I
> > tried to run REMD with two replicas, I got three output files:
> >
> > rem.out rem.out.000 and rem.out.001
> >
> > three mdinfo files:
> >
> > rem.mdinfo rem.mdinfo.000 and rem.mdinfo.001
> >
> > three trajectory files:
> >
> > md.traj md.traj.000 and md.traj.001
> >
> > and two restart fiels:
> >
> > rem.rstrt.000 and rem.rstrt.001
> >
> >
> >
> > Unfortunately, when I tried to run my own examples, I got problems.
> >
> > My system is a small dendron molecule. I built it by XLEaP.
> >
> > It seemed that AMBER8 REMD can run MD for this system, but
> several things
> > went wrong here.
> >
> > 1) I tried to run REMD with two replicas. But instead of three,
> I got only
> > two MD run results.
> >
> >
> >
> > Here are what I have:
> >
> > One topology file: prmtop
> >
> > two sander input file: rem.in.000 and rem.in.001
> >
> > two cordinates file: rem.r.000 and rem.r.001
> >
> > One PBS job file: olig8HelRGBREMD.Job
> >
> >
> > Here are what I got:
> >
> > Two output files: rem.out and rem.out.000
> > (I missed one more output file rem.out.001 here)
> >
> > Two trajectory files: rem.traj and rem.traj.000
> > (I missed one more trajecotry file rem.traj.001 here)
> >
> > Two mdinfo files: rem.mdinfo and rem.mdinfo.000
> > (I missed one more mdinfo file rem.mdinfo.001 here)
> >
> > Two restart files: rem.rstrt.000 and rem.rstrt.001
> > (But I have rem.rstrt.001 here)
> >
> >
> >
> > 2) In rem.out.000, I found input setup for this MD run is:
> > //////////////////////////////////////////////
> > File Assignments:
> > | MDIN: rem.in.001
> > | MDOUT: rem.out.000
> > |INPCRD: rem.rstrt.001
> > | PARM: prmtop
> > |RESTRT: rem.rstrt.001
> > | REFC: refc
> > | MDVEL: mdvel
> > | MDEN: mden.001
> > | MDCRD: rem.traj.000
> > |MDINFO: rem.mdinfo.000
> > |INPDIP: inpdip
> > |RSTDIP: rstdip
> > /////////////////////////////////////////////
> >
> > I really cannot understand why REMD use rem.in.001 for this run,
> > and still set output file with 000 extension.
> >
> >
> > 3) In olig8HelRGBREMD.log, two exchanges occurred. But both
> Temp0 and
> > NewTemp0 are 300.00K. However, in rem.in.000, I setup temp0 as
> 267.0 K, in
> > rem.in.001, I setup temp0 as 289.0 K. I didn't know where did
> sander get
> > 300.00 K as temp0.
> >
> > Here are my input and output files:
> >
> > olig8HelRGBREMD.Job:
> >
> > //////////////////////////////////////////////////////
> >
> > #PBS -N olig8HelRGBREMDtest.in
> > #PBS -l mem=50mw
> > #PBS -l walltime=933
> > #PBS -l nodes=2:ppn=1
> > #PBS -j oe
> > #PBS -m ae
> > #PBS -S /bin/csh
> >
> >
> > module load amber
> > setenv AMBERHOME /usr/local/amber/amber8
> >
> > cd /a/osu3112/work/test/amber8REMDbug/rem_gbrun05
> >
> >
> > set MDIN=rem.in <http://rem.in> <http://rem.in>
> > set MDOUT=rem.out
> > set MDINFO=rem.mdinfo
> > set PRMTOP=prmtop
> > set INPCRD=rem.r
> > set TRAJ=rem.traj
> > set RESTRT=rem.rstrt
> >
> > mpiexec /usr/local/amber/amber8/exe/sander.REM -O -ng 2 -rem 1
> > -remlog olig8HelRGBREMD.log -i $MDIN -o $MDOUT -inf $MDINFO -p
> > $PRMTOP -x $TRAJ -c $INPCRD -r $RESTRT
> >
> > //////////////////////////////////////////////////////
> >
> > rem.in.000:
> >
> > //////////////////////////////////////////////////////
> >
> > md9.in <http://md9.in> <http://md9.in> - PyrFurDuplex gb test
> run, igb = 1
> > &cntrl
> > imin = 0, nstlim = 5000, dt = 0.002,
> > ntx = 5, tempi = 0.0, temp0 = 267.0,
> > ntt = 1, tol = 0.000001, saltcon = 0.2,
> > ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
> > ntwx = 10, ntwe = 0, ntwr = 500, ntpr = 500,
> > scee = 1.2, cut = 99.0,
> > ntr = 0, tautp = 0.1, offset = 0.09,
> > nscm = 500, igb = 1, numexchg = 2,
> > irest = 1, ntave = 0,
> > /
> > //////////////////////////////////////////////////////
> >
> >
> >
> > rem.in.001:
> >
> > //////////////////////////////////////////////////////
> >
> > md9.in <http://md9.in> <http://md9.in> - PyrFurDuplex gb test
> run, igb = 1
> > &cntrl
> > imin = 0, nstlim = 5000, dt = 0.002,
> > ntx = 5, tempi = 0.0, temp0 = 289.0,
> > ntt = 1, tol = 0.000001, saltcon = 0.2,
> > ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
> > ntwx = 10, ntwe = 0, ntwr = 500, ntpr = 500,
> > scee = 1.2, cut = 99.0,
> > ntr = 0, tautp = 0.1, offset = 0.09,
> > nscm = 500, igb = 1, numexchg = 2,
> > irest = 1, ntave = 0,
> > /
> > //////////////////////////////////////////////////////
> >
> >
> >
> > Output file by PBS
> >
> > //////////////////////////////////////////////////////
> >
> > RUNNING MULTISANDER VERSION OF SANDER AMBER8
> > Total processors = 2
> > Number of groups = 2
> >
> > Looping over processors:
> > WorldRank is the global PE rank
> > NodeID is the local PE rank in current group
> >
> > Group = 0
> > WorldRank = 0
> > NodeID = 0
> >
> > Group = 1
> > WorldRank = 1
> > NodeID = 0
> >
> > //////////////////////////////////////////////////////
> >
> >
> >
> > Head of one output file rem.out:
> >
> > //////////////////////////////////////////////////////
> >
> >
> > -------------------------------------------------------
> > Amber 8 SANDER Scripps/UCSF 2004
> > -------------------------------------------------------
> >
> > | Run on 12/02/2005 at 14:24:03
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: rem.in.000
> > | MDOUT: rem.out
> > |INPCRD: rem.r.000
> > | PARM: prmtop
> > |RESTRT: rem.rstrt.000
> > | REFC: refc
> > | MDVEL: mdvel
> > | MDEN: mden.000
> > | MDCRD: rem.traj
> > |MDINFO: rem.mdinfo
> > |INPDIP: inpdip
> > |RSTDIP: rstdip
> >
> >
> > Here is the input file:
> >
> > md9.in <http://md9.in> < http://md9.in> - PyrFurDuplex gb test
> run, igb = 1
> > &cntrl
> > imin = 0, nstlim = 5000, dt = 0.002,
> > ntx = 5, tempi = 0.0, temp0 = 267.0,
> > ntt = 1, tol = 0.000001 , saltcon = 0.2,
> > ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
> > ntwx = 10, ntwe = 0, ntwr = 500, ntpr = 500,
> > scee = 1.2, cut = 99.0,
> > ntr = 0, tautp = 0.1, offset = 0.09 ,
> > nscm = 500, igb = 1, numexchg = 2,
> > irest = 1, ntave = 0,
> > /
> >
> > //////////////////////////////////////////////////////
> >
> >
> >
> >
> >
> > Head of one output file rem.out.000:
> >
> > //////////////////////////////////////////////////////
> >
> > -------------------------------------------------------
> > Amber 8 SANDER Scripps/UCSF 2004
> > -------------------------------------------------------
> >
> > | Run on 12/02/2005 at 14:25:02
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: rem.in.001
> > | MDOUT: rem.out.000
> > |INPCRD: rem.rstrt.001
> > | PARM: prmtop
> > |RESTRT: rem.rstrt.001
> > | REFC: refc
> > | MDVEL: mdvel
> > | MDEN: mden.001
> > | MDCRD: rem.traj.000
> > |MDINFO: rem.mdinfo.000
> > |INPDIP: inpdip
> > |RSTDIP: rstdip
> >
> >
> > Here is the input file:
> >
> > md9.in <http://md9.in> <http://md9.in> - PyrFurDuplex gb test
> run, igb = 1
> > &cntrl
> > imin = 0, nstlim = 5000, dt = 0.002,
> > ntx = 5, tempi = 0.0, temp0 = 289.0,
> > ntt = 1, tol = 0.000001, saltcon = 0.2,
> > ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
> > ntwx = 10, ntwe = 0, ntwr = 500, ntpr = 500,
> > scee = 1.2, cut = 99.0,
> > ntr = 0, tautp = 0.1, offset = 0.09,
> > nscm = 500, igb = 1, numexchg = 2,
> > irest = 1, ntave = 0,
> > /
> >
> > //////////////////////////////////////////////////////
> >
> >
> >
> > REMD log file:
> >
> > //////////////////////////////////////////////////////
> >
> > # replica exchange log file
> > # Replica #, Velocity Scaling Factor, T, Eptot, Temp0, NewTemp0
> > # exchange 1
> > 1 1.00 315.94 80.49 300.00 300.00
> > 2 1.00 306.34 89.22 300.00 300.00
> > # exchange 2
> > 1 1.00 292.12 88.27 300.00 300.00
> > 2 1.00 319.21 79.67 300.00 300.00
> > //////////////////////////////////////////////////////
> >
> >
> >
> > I also put all my REMD run related files in the attachment
> > remdrun.tar.gz except two trojectory files.
> >
> > Thank you so much in advance for help.
> >
> >
> > Best regards,
> > Peng Tao
> >
> >
> >
>
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