how did you determine these temperatures?
Peng Tao wrote:
> 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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Received on Sun Dec 18 2005 - 22:53:01 PST
