Dear Amber users,
I've been using iwrap=1 in my long simulations as recommended in the Amber 10 manual without any issues so far. However, I need to set up a new simulation where a subset of residues has to be restrained harmonically in the production with respect to the minimized coordinates. I'm restarting at every 1 ns and at each restart the reference for the restraint is the same minimized structure. My question is would wrapping the coordinates into the primary box interfere with the way restraining works? Here's my mdin:
&cntrl
iwrap=1, !crd and rst wrapped into a primary box
irest=1, !restart calculation
ntx=5, !X and V are read formatted, box info read as ntb=2
!constant T
temp0=300.0,
ntt=3, gamma_ln=1.0, ig=-1,
!constant P
ntb=2,
ntp=1,
!SHAKE
ntc=2,
ntf=2,
!restraint
ntr=1, restraintmask=':1-7,78,144,153,156-160,175-181,186 & .CA', restraint_wt=1.0 !kcal/mol/A2
!outputs
ntpr=500,
ntwr=50000,
ntwx=500,
nstlim=500000, dt=0.002
&end
END
Thanks!
Aysegul
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Received on Thu Aug 18 2011 - 18:00:03 PDT
