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 - 10:00:02 PDT
