AMBER Archive (2005)

Subject: AMBER: No exchange among replicas in REMD!

From: Peng Tao (amberhelp_at_gmail.com)
Date: Sun Dec 18 2005 - 16:11:06 CST

Dear all,

Sorry for the previous incomplete email. I accidentally clicked the send
button. Here I resend the email.

Thanks for the previous help on REMD in AMBER8.

Now I am trying to run REMD on of my systems. But in one REMD run with 12
replicas, I didn's see any exchange between any replicas pair when I set
numexchg as 200. I did set rem as 1, when I submitted REMD job.

I don't know if this is normal for REMD or not. I also want know how to
control how frequent the real exchanges happen during the REMD run. It seems
to me that REMD randomly chooses if there is exchange or not, and how many
pairs of replicas exchange temperatures. But it is not clear how to control
the frequency of these real exchanges. If my REMD run is correct, although
there is no real exchange at all, I don't how to deal with this situation.

I looked through the REMD log file, all the velocity scaling factors are -
1.00. And for every replica, Temp0 is always the same with NewTemp0. (which
means there is no temperature swap at all.)

Here is part of my REMD log file:
 # replica exchange log file
 # Replica #, Velocity Scaling Factor, T, Eptot, Temp0, NewTemp0
 # exchange 1
 1 -1.00 119.55 13.72 119.60 119.60
 2 -1.00 143.39 26.52 143.00 143.00
 3 -1.00 182.13 35.51 171.10 171.10
 4 -1.00 217.38 57.25 204.60 204.60
 5 -1.00 255.06 73.01 244.70 244.70
 6 -1.00 315.35 112.74 292.70 292.70
 7 -1.00 367.52 142.80 350.10 350.10
 8 -1.00 405.56 197.50 418.70 418.70
 9 -1.00 478.53 262.46 500.80 500.80
10 -1.00 616.29 309.58 598.90 598.90
11 -1.00 664.87 428.98 716.40 716.40
12 -1.00 886.69 473.05 856.80 856.80
 # exchange 2
 1 -1.00 126.53 1.07 119.60 119.60
 2 -1.00 144.11 11.69 143.00 143.00
 3 -1.00 172.42 35.45 171.10 171.10
 4 -1.00 211.65 56.20 204.60 204.60
 5 -1.00 248.05 71.46 244.70 244.70
 6 -1.00 299.63 121.81 292.70 292.70
 7 -1.00 365.56 129.09 350.10 350.10
 8 -1.00 405.90 196.33 418.70 418.70
 9 -1.00 536.35 225.19 500.80 500.80
10 -1.00 631.59 300.17 598.90 598.90
11 -1.00 688.14 415.64 716.40 716.40
12 -1.00 816.50 484.49 856.80 856.80
 # exchange 3
 1 -1.00 129.21 -3.06 119.60 119.60
 2 -1.00 140.18 13.43 143.00 143.00
 3 -1.00 168.73 41.04 171.10 171.10
 4 -1.00 202.73 59.59 204.60 204.60
 5 -1.00 220.75 96.92 244.70 244.70
 6 -1.00 289.10 126.19 292.70 292.70
 7 -1.00 348.22 145.64 350.10 350.10
 8 -1.00 416.76 209.61 418.70 418.70
 9 -1.00 486.43 247.08 500.80 500.80
10 -1.00 627.03 298.71 598.90 598.90
11 -1.00 741.25 359.00 716.40 716.40
12 -1.00 859.04 475.69 856.80 856.80
 # exchange 4
..................................
 # exchange 199
 1 -1.00 170.72 27.97 171.10 171.10
 2 -1.00 139.51 12.05 143.00 143.00
 3 -1.00 233.27 80.45 244.70 244.70
 4 -1.00 404.01 194.87 418.70 418.70
 5 -1.00 120.86 -6.87 119.60 119.60
 6 -1.00 188.12 64.80 204.60 204.60
 7 -1.00 301.06 93.25 292.70 292.70
 8 -1.00 341.35 143.01 350.10 350.10
 9 -1.00 666.16 416.24 716.40 716.40
10 -1.00 529.22 229.41 500.80 500.80
11 -1.00 821.64 504.87 856.80 856.80
12 -1.00 572.81 312.77 598.90 598.90
 # exchange 200
 1 -1.00 167.26 31.97 171.10 171.10
 2 -1.00 139.68 11.45 143.00 143.00
 3 -1.00 250.46 71.16 244.70 244.70
 4 -1.00 397.55 191.23 418.70 418.70
 5 -1.00 119.41 -5.27 119.60 119.60
 6 -1.00 207.08 54.04 204.60 204.60
 7 -1.00 269.13 111.53 292.70 292.70
 8 -1.00 355.21 134.04 350.10 350.10
 9 -1.00 703.99 383.90 716.40 716.40
10 -1.00 468.44 275.86 500.80 500.80
11 -1.00 834.90 498.02 856.80 856.80
12 -1.00 563.73 326.88 598.90 598.90

Part of my PBS job file:

set MDIN=olig9HafHelGBREMD.in
set MDOUT=olig9HafHelGBREMD.out
set MDEN=olig9HafHelGBREMD.mden
set MDVEL=olig9HafHelGBREMD.mevel
set MDINFO=olig9HafHelGBREMD.mdinfo
set PRMTOP=olig9hafhelBondi.top
set INPCRD=olig9HafHelGBMDeq.restrt
set TRAJ=olig9HafHelGBREMD.traj
set RESTRT=olig9HafHelGBREMD.restrt

mpiexec /usr/local/amber/amber8/exe/sander.REM -O -ng 12 -rem 1 -remlog
olig9HafHelGBREMD.log -i $MDIN -e $MDEN -o $MDOUT -v $MDVEL -inf $MDINFO
-p $PRMTOP -x $TRAJ -c $INPCRD -r $RESTRT -ref $INPCRD

I also attached most of my REMD related files for further diagnoses.
Thanks in advance for your help.

Best regards,
Peng Tao
The Ohio State Univeristy


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