AMBER Archive (2008)

Subject: Re: AMBER: replica exchange with amber9

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Sep 23 2008 - 17:52:04 CDT

not sure if this is the problem, but amber9 needed irest=1 for REMD. it
should have complained. (note that you list irest=0 twice, so change both).
if you're going to do a lot of REMD, amber10 is really worth getting as the
REMD is much cleaner and more functional.
mail back if those don't solve it.

On Tue, Sep 23, 2008 at 6:44 PM, <greddy1_at_umd.edu> wrote:

> Hello all,
> I am relatively new to AMBER. I have used the tutorials which are excellent
> to get
> myself acquainted with the software. Right now I am trying to do a replica
> exchange simulation of a peptide using amber9. I am running into problems.
> The simulation stops after the first exchange. I have used the tutorial on
> the
> Amber web page for replica exchange which is for version 10. Probably, this
> is
> causing some problems. Can any one help me figure out the problem or point
> me to a tutorial for replica exchange using amber9.
> Thanks
> Greddy
>
> My input script for the tutorial:
>
> pep replica exchange simulation
> &cntrl
> irest=0, ntx=1,
> nstlim=5000, dt=0.002,
> irest=0, ntt=3, gamma_ln=1.0,
> temp0=XXXXX, ig=RANDOM_NUMBER,
> ntc=2, ntf=2, nscm=1000,
> ntb=0, igb=5,
> cut=12.0,
> ntpr=5000, ntwx=5000, ntwr=5000,
> nmropt=1,
> numexchg=2500
> /
> &wt TYPE= END
> /
> DISANG=pep_cap_amber_chir.dat
> *****************************************************
> Log file output:
>
> # replica exchange log file
> # numexchg is 2500
> # Replica #, Velocity Scaling, T, Eptot, Temp0, NewTemp0, Success rate
> (i,i+1)
> # exchange 1
> 1 -1.00 0.00 -697.55 270.00 270.00 0.00
> 2 -1.00 0.00 -724.27 281.32 281.32 0.00
> 3 -1.00 0.00 -711.78 293.12 293.12 0.00
> 4 -1.00 0.00 -660.99 305.41 305.41 0.00
> 5 -1.00 0.00 -613.79 318.22 318.22 0.00
> 6 -1.00 0.00 -618.67 331.56 331.56 0.00
> 7 -1.00 0.00 -594.27 345.47 345.47 0.00
> 8 1.02 0.00 -538.81 359.95 375.05 2.00
> 9 0.98 0.00 -565.57 375.05 359.95 0.00
> 10 -1.00 0.00 -470.63 390.78 390.78 0.00
> 11 -1.00 0.00 -446.30 407.16 407.16 0.00
> 12 -1.00 0.00 -441.40 424.24 424.24 0.00
> 13 -1.00 0.00 -375.77 442.03 442.03 0.00
> 14 -1.00 0.00 -410.95 460.56 460.56 0.00
> 15 -1.00 0.00 -370.95 479.88 479.88 0.00
> 16 -1.00 0.00 -353.13 500.00 500.00 0.00
> ****************************************************************
> Result part of the output for one of the replicas:
> -------------------------------------------------------------
> -------------------
> 4. RESULTS
> -------------------------------------------------------------
> -------------------
>
>
> NSTEP = 0 TIME(PS) = 5000.000 TEMP(K) = 0.00 PRESS =
> 0.0
> Etot = -697.5475 EKtot = 0.0000 EPtot =
> -697.5475
> BOND = 94.0549 ANGLE = 227.8215 DIHED =
> 178.6298
> 1-4 NB = 104.4641 1-4 EEL = 1802.5777 VDWAALS =
> -170.8794
> EELEC = -2354.0564 EGB = -580.4516 RESTRAINT =
> 0.2922
> EAMBER (non-restraint) = -697.8396
> -------------------------------------------------------------
> -----------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.292
> =================================================
> ==============================
> Exiting runmd after getting initial energies for REMD 0
>
> ***************************************************************
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