Dear Sir
Thanks for reply. I m also confused. I have 2080 frames for 1040 ps(total simulation).
total frames is ok but as I found I need to change the time interval in the ptraj command. i changed ptraj command as:
trajin heat1.crd
trajin eq1.crd
trajin md1.crd
strip :WAT
rms first mss out rms1.dat time 0.5 .CA,C,N
atomicflubtuation out rmsf1.dat :1-388 byres
go
but the problem of dumping continues.
I run this simulation.could anyone tell me what causes this dumping?It can be from the intial structure?or any thing else...
# Heating to 300 K with constant volume
&cntrl
imin=0, irest=0,
ntpr=50, ntwr=1000, ntwx=500, iwrap=1,
ntr=1, ntx=1, tol=0.00001,
ntb=1, igb=0, ntp=0,
ntt=3, GAMMA_LN=1.0, tempi=0.0, temp0=300.0,
nstlim=20000, dt=0.001, cut=10.0,
/
# keep protein fixed with weak restraint
3.0
RES 1 390
END
END
# Initial MD equilibration with constant pressure
&cntrl
imin=0, irest=1,
ntpr=50, ntwr=1000, ntwx=500, iwrap=1,
ntx=7, ntc=2, ntf=2, tol=0.0000001, ntb=2, igb=0,
ntt=1, tautp=0.2, temp0=300.0,
ntp=1, pres0=1.0, taup=0.8,
nstlim=20000, dt=0.001,
cut=10.0
&end
END
# MD production with constant pressure
&cntrl
imin=0, irest=1,
ntpr=50, ntwr=1000, ntwx=500, iwrap=1
ntx=5, ntf=2, ntc=2, tol=0.00001, ntb=2, igb=0,
temp0=300.0,
ntp=1, pres0=1.0, taup=0.2,
nstlim=1000000, dt=0.001,
ntt=3, gamma_ln=1.0,
cut=10.0
&end
END
---------------------------------
We have the perfect Group for you. Check out the handy changes to Yahoo! Groups.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Nov 08 2006 - 06:07:29 PST
