Re: Belly option in sander

From: David Case <>
Date: Wed 31 Jan 2001 11:28:43 -0800

On Wed, Jan 31, 2001, Florian Barth wrote:

> I would like to run a md simulation in sander using the belly option to
> constrain the protein backbone. This is my
> #50ps simulated annealing with temp. ramp and Belly
> &cntrl
> nstlim=25000, dt=0.002, ntt=1, ibelly=1, igb=3, ntb=0, ....
> &end

> "When igb>0, the moving part must be at the start of the molecule.
> This does not seem to be the case here."
> Does anybody know, how the or the topology files must be altered
> to run above simulation in sander. A colleague pointed out to me,
> that it is possible with
> sander_classic to run belly simulations but I would like to stick to
> the "new" sander.

I'm sending this response to the whole list, since this point may be
confusing to many people.

If you are simulating a non-periodic system with ordinary Coulomb or
distance-dependent dielectric (as above: ntb=0,igb=3), in almost all
circumstances you should sander_classic rather than sander. Sander_classic
is both more flexible and faster for these sorts of calculations.

People should not assume that "new" sander is somehow better that
sander_classic. Eventually we will be able to remerge the codes, but for
now, as a rule of thumb:

For periodic simulations with PME, and for non-periodic simulations with
generalized Born: use sander.

For all other non-periodic simulations, and to use OWFEG, use

If you really want to run a periodic simulation without PME (i.e. with
cutoffs instead), use sander_classic; (in my personal view, however,
this sort of simulations is not generally to be recommended.)

It would clearly be better if we had one program that was "good" at
everything, and apologize for any confusion that the current situation
leads to.

...hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Wed Jan 31 2001 - 11:28:43 PST
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