AMBER Archive (2005)

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

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Fri Dec 02 2005 - 16:49:25 CST

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>)
> Replica exchange (REM) test suite for Amber 8:
> 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>
> 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> - 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> - 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> - 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> - 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
>
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu