AMBER Archive (2007)

Subject: Re: AMBER: Distance restraints between center of mass of two molecules

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Aug 15 2007 - 10:52:27 CDT

On 8/15/07, Sudha Mani Karra <karra.md_at_gmail.com> wrote:
> Hey Carlos,
> Thank you.
> If you are familiar with the distance restraints, could you help me in
> uderstanding the following?
>
> The md input file is
>
> &cntrl
> imin=0, irest=1, ntx=7,.......,
> .........,
> &end
> &rst iat=1, 6, r1=0.0, r2=..., r3=..., r4=...,
> rk2=....,rk3=.....
> &end
> In the above, for simple harmonic restraints we take r1=0.0 ,r2=r3 and r4 to
> be a large value.

correct

> IF my R is say around 8 A then what should be the r2, r3 and r4 values?

you mean R is your target distance? then use r2=8, r3=8, r4=100

> Also the force constants rk2 and rk3? Which force consant should be used in
> calculating the harmonic potential?

it depends on how much fluctuation you want, stronger restraints keep it closer
to the r2/r3 values. put in a sample force constant (say 1) and
calculate how much
distance change you can get for ~0.5-1 kcal/mol, which is what you're going
to get at 300K. values of 0.1 to 10 are probably most useful. too
small and it won't
keep it restrained, too large and you'll get instability in the
simulation since the
frequency of the motion will be too fast for the time step.

> Appreciate your help.
> Sudha
>
>
> 

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