AMBER Archive (2008)

Subject: Re: AMBER: multiple dihedral restraints using group (in Amber 10)

From: fatima.chami_at_durham.ac.uk
Date: Wed Jun 18 2008 - 05:05:40 CDT

Quoting mkseo <seo_at_ualberta.ca>:

>
> Hello Amber users,
>
> I tried to calculate the potential of mean force of the dissociation
> of protein-sugar complex using umbrella sampling.
> I added six restraint potentials (distance, angles and dihedral
> restraints) with defining by a group of atoms. (this kind of restraint
> is provided in Amber 10)
>
> The magnitude of the force constants for each restraint potential was
> estimated from the fluctuations of its associated coordinates as k_x =
> k_BT/<delta x^2>.
> Langevin thermostat was used to maintain constant temperature (see the
> input below)
>
> INPUT:
> Dynamic Simulation with Constant Temperature
> &cntrl
> ntwe =500, ntwx =500, ntwv =500, ntpr =500,
> ntt =3, temp0 =300.0, tempi =300.0,
> gamma_ln = 60.0,
> scnb = 2.0, scee = 1.2,
> ntb =0, ntc =2, ntf =1, cut=9999.0,
> nstlim =150000, dt =0.001,
> irest =1, ntx =5,
> nmropt =1,
> /
> &wt type ='DUMPFREQ', istep1=1 /
> &wt type='END' /
> DISANG = restraints_5.0.in
> DUMPAVE = native_T300_d_vs_t.5.0
> LISTOUT = POUT
>
>
>
> But, I have the following error message.
>
> The system has extended beyond
> the extent of the virtual box.
> Restarting sander will recalculate
> a new virtual box with 30 Angstroms
> extra on each side, if there is a
> restart file for this configuration.
> SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
> Atom out of bounds. If a restart has been written,
> restarting should resolve the error

Hi,
I think there is a problem with your restart file (irest =1) did you get this
initial configuration from a periodic MD run ...

cheers
Fati.

>
>
> Can anyone help to solve this problem?
> What is wrong with my simulation, force constants or thermostat
> parameters?
>
> Thanks
>
> Mikyung
>
>
>
>
>
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> 

-- 
Dr. F.Chami
Science Lab.
Department of Chemistry
Durham University
South Road Durham, DH 1 4 LE
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