AMBER Archive (2006)

Subject: Re: AMBER: sander ntc=2 ntf=1

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Dec 19 2006 - 05:39:38 CST

Nick,
- you can use ntc=2 and ntf=1, that is fine
- you should find out why ntf=2 doesn't work (does it work for normal MD?)
  do you think shake might be failing for high T replicas?
  do you have access to the stdout files to see if there is a
   shake failure msg for one of the replicas (then the others will hang)?
- I strongly recommend against using ff99. use ff99SB or ff03.
good luck
carlos

Nicolas Lux Fawzi wrote:

> If I'm running an amber9 sander ff99 protein + TIP3P (or TIP4P) water
> REMD simulation ntc=2 ntf=2, I get a problem on AIX and opteron
> platforms.
>
> My question is, can I run with ntc=2, ntf=1, which seems to work?
> Will this give the "correct" and expected output. As for the errors
> with ntc=ntf=2, I just get "terminated" mpi signal... I suspect if
> might be some type of MPI timeout. On an opteron with infiniband (i
> don't know which MPICH but it's NERSC's jacquard which Bob Duke is
> familiar with), I was getting VAPI timeout errors, which may be fixed
> with changing the timeouts and retries... see the output below
>
> Please let me know if you have any insight on if ntc=2, ntf=1 is
> appropriate.
> -Nick
>
>
> bash-2.05b$ cat mdinremd.1
> sander input for TIP3P plus peptide MD
> &cntrl
> nstlim = 1000,
> ntx = 5,
> irest=1, iwrap = 1,
> ntt = 2,
> temp0 = 270
> ntc = 2,
> ntb = 1,
> ntf = 1,
> cut = 9.0,
> ntwx = 500,
> numexchg = 4000,
>
> /
>
> &ewald
> ew_type = 0,
> skinnb = 2.0,
> /
>
> END
> END
> _________________________________________
>
> from the standard output of an AIX loadleveler job:
>
> Group = 14
> WorldRank = 14
> NodeID = 0
>
> Group = 15
> WorldRank = 15
> NodeID = 0
>
>
> NSTEP = 400 TIME(PS) = 19465.400 TEMP(K) = 412.19 PRESS
> = 0.0
> Etot = -11501.2579 EKtot = 4008.6951 EPtot =
> -15509.9530
> BOND = 25.7644 ANGLE = 79.2867 DIHED
> = 79.8073
> 1-4 NB = 29.9351 1-4 EEL = 629.7989 VDWAALS =
> 2454.6631
> EELEC = -18809.2085 EHBOND = 0.0000 RESTRAINT
> = 0.0000
> Ewald error estimate: 0.8865E-05
>
> ------------------------------------------------------------------------
> ------
>
> ERROR: 0031-250 task 6: Terminated
> ERROR: 0031-250 task 31: Terminated
> ERROR: 0031-250 task 46: Terminated
> ........................
>
>
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