AMBER Archive (2007)

Subject: AMBER: problem in implcit simulation

From: gurpreet singh (gps.iitm_at_gmail.com)
Date: Wed Mar 28 2007 - 22:25:53 CST

hello Amber users

i am using sander module of Amber9 to carry out the implcit MD simulation
for my protein , since i m new to implicit simulations so i dont know
exactly the time scales of these simulations but one thing which i am very
sure about is that implicit shud take less time as compared to the explicit
simulation but in my case opposite is happening,implicit mini is taking lot
more time as comapred to explicit, i started my simulation with the
minimization by putting restraint on all the heavy atoms and allowed
hydrogen atoms to move freely, same rpoblem i observed in equilibration run
which i carried after this mini

i m giving my mini file flags please tell me that this problem of more time
is comin because of some particular flag i mnetioned in the input file or
because of some other problem

mini file :
imin=1,igb=2,cut=20.0,maxcyc=500,ncyc=250,ntr=1,intdiel=1.0extdiel=
78.5,ntb=0

equilibration file: imin=0,igb=2,cut=20.0,ntr=1,intdiel=1.0
extdiel=78.5,ntb=0,nstlim=20000,
dt=0.002,ntc=2,ntf=2,tempi=10.0,temp0=300.0,ntt=1,tautp=2.0,ntp=0,ntpr=100,
ntwx=0

please reply soon
 thanks

Gurpreet Singh
IIT MADRAS
INDIA

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