Re: AMBER: Dynamics and Simulated Annealing

From: Teletchéa Stéphane <steletch.biomedicale.univ-paris5.fr>
Date: 25 Jul 2003 18:57:53 +0200

Le ven 25/07/2003 à 15:03, Narang Manpreet Kaur a écrit :
> Dear AMBER users,
> I have done minimization on the drug molecule
> folllwed by molecular dynamics at constant temperature of 300K. Now I want
> to perform the molecular dynamics by raising the temperature from 300
> to 500K and then cool the system back to 300K. I have not given any
> NMR restraints for the system i.e.nmropt=0.
>
> -----------------------------------------------------------------------------------------------------------------------------------------------
> Here is my input file:
> &cntrl
> imin=0, cut=9.0, nstlim=4500, temp0= 300, tempi=500,
> ntb=1, scee=1.2, ntx=7, irest=1, ntwe=100, ntwx=100, ntwe=100 ntpr=100,
> vlimit=20
> &end
> &wt type='TEMP0', istep1=0,istep2=1500,value1=300.0,
> value2=500.0, &end
> &wt type='TEMP0', istep1=1500,istep2=4500,value1=500.0,
> value2=500.0, &end
> &wt type='END' &end
>
> &wt type='TAUTP', istep1=0,istep2=1500,value1=0.2,
> value2=0.2, &end
> &wt type='TAUTP', istep1=1500,istep2=4500,value1=4.0,
> value2=2.0, &end
> &wt type='END' &end

[SNIP]
> -------------------------------------------------------------------------------
> The tempearature has not reached the desired 500K and back to 300 in
> fact it was between 275-280 in the entire run. I want to know how this can
> be achived in vaccuum and in water. The file input given is for the
> molecule in water.
> Any help in this regard will be appreciated

Assuming you are using amber7, i'll try if i were you to increase the
time taken to go to your temperature.

if you want to force it, you could switch to NTT=4 but being cautious of
energy drops coming from the rescaling of velocities (you may consider
VRAND parameter also).

Stef

-- 
Teletchéa Stéphane <steletch.biomedicale.univ-paris5.fr>




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Received on Fri Jul 25 2003 - 18:53:00 PDT
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