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 md.in:
>
> #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 md.in 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
sander_classic.
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: case_at_scripps.edu
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 | http://www.scripps.edu/case
==================================================================
Received on Wed Jan 31 2001 - 11:28:43 PST
