AMBER Archive (2009)

Subject: Re: [AMBER] neb error while heating

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Dec 28 2009 - 11:34:56 CST

how did you generate the initial structures? what is the conformational
change? are you sure that the initial guess for the path is reasonable? have
you looked at the restart files from the intermediate points on the path?

On Sat, Dec 26, 2009 at 10:09 PM, balaji nagarajan <balaji_sethu_at_hotmail.com
> wrote:

>
>
> Dear Amber !
>
> I am doing The Nudged Elastic Band Approach to Finding the Lowest
> Energy
>
> Pathway Between two States for the DNA being in two different energy states
> ,
> i saw the tutorial which have been done for the alanine dipeptide
>
> I have generated the 50 images . I tried heating the system
> I have the input file as follows
> -------------------------------------
>
> heating the system
> &cntrl
> imin = 0, irest = 0,
> ntc=1, ntf=1,
> ntpr=50, ntwx=5,
> ntb = 0, cut = 12.0, rgbmax=12.0,
> igb = 1, saltcon=0.2,
> nstlim = 40000, nscm=0,
> dt = 0.00001,
> ntt = 3, gamma_ln=100.0,
> tempi=0, temp0=300,
> ineb = 1,skmin =0.1,skmax = 10,
> nmropt=1
> /
> &wt type='TEMP0', istep1=0,istep2=35000,
> value1=0.0, value2=300.0
> /
> &wt type='END'
> /
> -------------------------------
> when i gave the sander.PIMD run i got error as
> Error in diagonalization routine dgeev
> Error in diagonalization routine dgeev
> Error in diagonalization routine dgeev
> Error in diagonalization routine dgeev
> Error in diagonalization routine dgeev
> Error in diagonalization routine dgeev
> Error in diagonalization routine dgeev
> Error in diagonalization routine dgeev
> Error in diagonalization routine dgeev
> Error in diagonalization routine dgeev
> Error in diagonalization routine dgeev
> Error in diagonalization routine dgeev
> ---------------------------------------------------
>
>
> how to solve this any thing have to be changed in the input
>
> regards
> balaji
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