AMBER Archive (2007)

Subject: Re: AMBER: QM/MM Umbrella sampling

From: Jerome.GOLEBIOWSKI_at_unice.fr
Date: Sat Apr 28 2007 - 02:55:49 CDT

Hi.
r1 and r4 should be very different from r2 and r3 if you want your potential to
be harmonic. I would suggest r1 = 0.0 and r4 = 99.0.
Your force constant is indeed 200 kcal/(mol.A²), since the amber format for this
 term is k(x-x0)² and not 1/2K(x-x0)².
Good luck.
Jerome

Selon Jason DeChancie <jdechanc_at_chem.ucla.edu>:

> Using Amber 9, I'm trying to run an umbrella sampling calculation with
> a combined QM/MM potential for a reaction along a carbon-carbon bond.
> Here is an example of an input file for one window:
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 12, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 1, tautp = 1.0,
> nstlim = 50000, dt = 0.001,
> ntpr = 100, ntwx = 100, ntwr = 100,
> ifqnt=1, nmropt=1
> /
> &qmmm
> qmmask=':187',
> qmcharge=-2,
> qmtheory=2,
> qmshake=0,
> qm_ewald=1, qm_pme=1
> /
> &wt type='DUMPFREQ', istep1=100 /
> &wt type='END' /
> DISANG=c_c-11.RST
> DUMPAVE=am1_c_c_vs_t.11
>
> were the restrain file c_c-11.RST reads: &rst iat=3135,3144, r1=1.0,
> r2=2.3, r3=2.3, r4=4.0, rk2=100., rk3=100., /
>
> My question pertains to the restraint file. Are these reasonable
> values for r1 and r4 to obtain a harmonic biassing potential, with a
> minimum of 2.3 Å. Is the force constant defined here as 2 X 100 = 200
> kcal mol-1 Å-2?
>
> Thanks!
>
> Jason DeChancie
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
Jérôme Golebiowski, Ph D.
Lab CMBA, University of Nice Sophia Antipolis
06108 nice cedex 2
France
tel: +33 (0)4 92 07 61 03
http://www.unice.fr/lcmba
http://www.unice.fr/lcmba/golebiowski
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu