AMBER Archive (2005)

Subject: AMBER: Replica-Exchange MD from AMBER8!

From: Peng Tao (amberhelp_at_gmail.com)
Date: Fri Dec 02 2005 - 16:28:27 CST

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)
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
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 - 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 - 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 - 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 - 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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