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----- Forwarded message ----- From: "Saikat Pal" <saikatpaliitg.yahoo.com> To: "AMBER Mailing List" <amber.ambermd.org> Cc: Sent: Wed, 12 Sep 2018 at 12:39 PM Subject: Query for umbrella sampling Dear all,I want to calculate the PMF of two peptides. I want to pull two atoms along the Z axis. I want to know is my input is correct or not ?:4000 step minimization for 15 ang
#minimisation
&cntrl
imin = 1,
maxcyc=4000, ncyc = 1000,
ntpr = 100, ntwr = 1000,
ntf = 1, ntc = 1, cut = 10.0,
ntb = 1, ntp = 0,
nmropt = 1,
&end
&wt
type='END',
&end
DISANG=disang.15
#equilibration1000 ps NPT equilibration for 15 ang
&cntrl
imin = 0, ntx = 1, irest = 0,
ntpr = 5000, ntwr = 50000, ntwx = 0,
ntf = 2, ntc = 2, cut = 10.0,
ntb = 2, nstlim = 500000, dt = 0.002,
tempi=0.0, temp0 = 298.0, ntt = 3,
gamma_ln = 1.0,
ntp = 1, pres0 = 1.0, taup = 5.0,
nmropt = 1, ioutfm=1,
&end
&wt
type='END',
&end
DISANG=disang.15
#production10 ns NPT production for 15 ang
&cntrl
imin = 0, ntx = 5, irest = 1,
dielc=1.0,cut=10.0,
ntt=1,temp0=298.0,tautp=0.1,
ntp=1,ntb=2,ntc=2,ntf=2,
iwrap=1,nstlim=5000000,dt=0.002,
ntwx=1000,ntpr=500,nmropt=1,
pres0 = 1.0,
&end
&wt
type='DUMPFREQ', istep1=10,
&end
&wt
type='END',
&end
DISANG=disang.15
DUMPAVE=distance_15.dat
#disang#Harmonic restraints for 15 ang
&rst
iat=-1,-1,
iresid=1,
r1=-99.00000, r2=15.00000, r3=15.00000, r4=99.00000,
rk2=6.0, rk3=6.0,
igr1=6,0,
igr2=1,1,0,
grnam1(1)='O14',
grnam2(1)='N1',grnam2(2)='N3',
/
Thanks and Regards,
Saikat Pal
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Received on Wed Sep 12 2018 - 14:00:02 PDT
