Dear Amber users/developers!
I am preparing some work with gibbs; however there are some issues I
could not clarify from the manuals and literature:
1. Particle Mesh Ewald:
The manual says:
"As yet, there is not much experience with the PME in Gibbs, so it
should be considered an experimental option. ... It has been tested
only with "standard" window growth"
Did this situation change in the meantime? I would definitely like to
use TI+PME+DynModW!
2. Treatment of vanishing atoms:
- Is there a recommended value or range for IDSX0 (factor for the
mixed VdW radii)?
- There seems to have been some controversy about the shrinking of
bonds to dummy atoms in order to improve sampling. Is it now
generally recommended to shrink those bonds or to leave them as they
are?
- In the AMBER FAQ I found that - if bond shrinking is employed at
all - the length of the bond should not be decreased below ~0.2 Ċ
for stability reasons. This is explained in terms of an increased
frequency of the corresponding valence vibration. I would like to
understand, why this frequency changes at all when only the
equilibrium bond length is changed but the force constant is not.
3. Control of sampling and convergence:
- I thought that in order to estimate if the simulation hat already
sufficiently sampled phase space at a certain value of l
("l"="\lambda") it might be a good idea to monitor the "running
values" of dV/dl and <dV/dl> (for TI). However, there are only the
final values of <dV/dl> for each l printed in the POUT file. Did I
not find the necessary input flag, is this not implemented, or am I
somehow conceptually wrong here?
- Is it possible to write a restart file at the end of each \lambda
interval, so if one decides to simulate for some more time one can
start again there and does not loose the previously accumulated
values of <dV/dl> ?
- I suppose that the default control parameters for the DynModWin
algorithm are safe to start with. If not, what parameter should be
given a differnt value?
- Is there any experience concerning the necessary steps for
equilibration and data collection for a "minor" mutation (GLN->ASN)
in a protein (using PME+DynModWin)?
Thanks in advance for your advice!
Michael
--
Dr. Michael Jakusch
ETH - Swiss Federal Institute of Technology
Departement of Applied Biosciences
Winterthurerstrasse 190
CH-8057 Zürich
Switzerland
Phone: +41.1.635 60 71
Fax: +41.1.635 68 84
email: michael.jakusch_at_pharma.anbi.ethz.ch
Received on Thu Sep 20 2001 - 05:39:47 PDT
