Dear ambers
This is probably something that I should know...
I have a 6 aminoacids long peptide which i want to run a simulated
annealing on, that is simply generate lots of random conformations. I have
a script that i use to generate a series of inputfiles and then I run
these identical inputfiles. What then happens is that all structures that
are generated are identical! I thought that the start velocities in an MD
run are supposed to be random, and hence follow different trajectories...
What have i done wrong?
Here is the input:
&cntrl
imin=0, nmropt=1,
ibelly=0, ntr=0,
ntx=1, ntpr=1000, ntwx=0, ntwv=0, ntwe=0,
ntf=2, ntc=2,
ntb=1, ntp=0,
dielc=1, cut=8.0, nsnb=10.0,
scnb=2.0, scee=1.2,
nstlim=25000, dt=0.001,
temp0=300, tempi=300, ntt=4, tautp=0.2,
&end
&wt type='TEMP0',
istep1=1, istep2=1000,
value1=300, value2=300,
&end
&wt type='TEMP0',
istep1=1001, istep2=5000,
value1=300, value2=1500,
&end
&wt type='TEMP0',
istep1=5001, istep2=20000,
value1=1500, value2=1500,
&end
&wt type='TEMP0',
istep1=20001, istep2=23000,
value1=1500, value2=0,
&end
&wt type='END',
&end
Arvid Soderhall
Received on Fri Nov 08 2002 - 04:35:23 PST
