parto haghighi wrote:
Dear GMX users,
when I want to correct charge group of one molecule I have to do
calculate its free energy.
I did this work by applying 6th gromacs tutorial.
In this tutorial user has to assign 0 value in topology:
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 opls_138 1 ALAB CB 1 0.000 12.011
2 opls_140 1 ALAB HB1 2 0.000 1.008
3 opls_140 1 ALAB HB2 3 0.000 1.008
4 opls_140 1 ALAB HB3 4 0.000 1.008
5 opls_140 1 ALAB HB4 5 0.000 1.008
my question is when I have to zero value to its charge how can I correct my
charges:
Don't set your charges to zero. The tutorial states why everything is zero
there - the process for which the free energy calculation is being done is a van
der Waals transformation, so the charges are fixed at zero. For your
calculations, you need to:
1. assign some starting value for charges (QM, chemical intuition, etc) and atom
types
2. calculate DG of solvation and check the accuracy of the resulting value
3. adjust charges (and perhaps atom types) if necessary and return to step 1
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
