Have you run exactly the same input but using normal not read?
On Jun 25, 2012 12:48 PM, "Do Yong Kim" <kdy2002.gmail.com> wrote:
> Hello Amber Users,
>
> I am following REMD AMBER tutorial with a 15 amino acid peptide, and I am
> running in to some problems right now.
>
> I made prmtop and inpcrd files from xleap by loading preexisting pdb file
> that I have.
>
> After this I made minimization file and followed the instructions on the
> tutorial and using the same conditions as the tutorials have. Up to this
> point the equilibrated structures looks normal, no non-sense bond distance
> nor close atoms present. However, when I do the remd, the
> resulting structures from the simulation, the structures basically blow up,
> resulting blobs of atoms. I have played with cut and rgbmax but no useful
> results were obtained.
>
> Did anyone encounter these problems before? any help will be greatly
> appreciated.
>
> I am using these input parameters for my remd
>
> &cntrl
> irest=0, ntx=1,
> nstlim=500, 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=75.0, rgbmax=50.0,
> ntpr=100, ntwx=1000, ntwr=100000,
> nmropt=1,
> numexchg=1000,
> /
> &wt TYPE='END'
> /
> DISANG=372-3_chir.dat
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Received on Mon Jun 25 2012 - 10:00:03 PDT
