Hi,
Yes, my fault, I completely forgot about the average DV/DL breakdown at the end of the mdout file. The last 3 months I have been running FEP calculations and then I had to visit the TI results after that time.
1) When I run new TI calculations then I will select idecomp=1.
2) That was the reason to do the calculations in both ways, removing the charges of the entire molecule or only in certain atoms. In the first situation I avoid the formal charge in the cell (and the lattice problems) but I am creating a big perturbation in the entire molecule. In the second situation I only do a small perturbation in a certain numer of atoms but then I create a series of intermediate steps with formal charge (then modifing the interaction with solvent and conformational behaviour). We have to decide what option is better.
Thank you very much for your help, Thomas.
Kepa K.
***************************************************************************************************
________________________________
De: "steinbrt.rci.rutgers.edu" <steinbrt.rci.rutgers.edu>
Para: Kepa K. Burusco <kekoburgo.yahoo.es>; AMBER Mailing List <amber.ambermd.org>
Enviado: Lunes 28 de enero de 2013 13:10
Asunto: Re: [AMBER] TI alpha-beta glucose Glycam06h
Hi,
> the calculation again activating the DVDL energy decompostion to check the
> breakdown.
The calculations you already did should have a dvdl breakdown at the end
of mdout, idecomp just breaks it down further by residue etc IIRC.
> 1) According to the amber manual, the "idecomp" options to switch on the
> DVDL breakdown are "=1" and "=2". The first option adds the 1-4 non bonded
> energies to the internal energies, and the second option to the EEL and
> VDW. In my particular case, it seems that the best option would be
> selecting "idecomp=2" (not sure anyway). Actually, I'm wondering in what
> situations is better so select option 1 or 2. Could you please give any
> advice/reference about this?
I would consider 1-4 interactions to be internal energies, so I dont see
when option 2 would be useful. Anyway, no matter how you decompose them,
the huge energies from individual substeps of a TI calculation can not be
interpreted in a meaningful way. However, you can rationalize them in
terms of what contributions in the force field they come from.
> 2) At the beginning I was running my tests in two different ways: In the
> first one, I switched off/on ALL the charges in the glucose molecule, and
...
> really non-negligible. So, do you think it is better to switch off/on all
> the charges in the molecule as I do rather
> than only the charges in the mutated atoms as in the tutorial?
Other people may have different opinions here, but I believe that running
with non-zero or even fractional charges is not a problem per se in MD.
For TI it is almost unavoidable. So I would not worry about net charge and
instead keep the perturbation as small as possible, so change only these
charges that have to change. For Glucose, you are effectively making it a
very nonpolar molecule and then repolarize it by removing/adding all
charges, which seems an inefficient way to change a small part of the
molecule.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 28 2013 - 10:30:02 PST
