On 5/18/12 4:21 PM, Rustad, James R wrote:
Dear GMX users,
I cannot figure out from the manual whether it is possible to use tabulated
non-bonded potentials in a BAR calculation.
I want to estimate the free energy for changing Fe2+ to Fe3+. These have
different charges, of course, and also different non-bonded interactions. These
non-bonded interactions are neither LJ nor Buckingham, so I am using a lookup
table (table_O_Fe2.xvg and table_O_Fe3.xvg) for the “vdw” part (vdw_type=User).
I think I should be able to define Fe2 and Fe3 atoms types, and associate the
tables (table_O_Fe2.xvg and table_O_Fe3.xvg) with those types in the mdp file:
energygrps = O Si Na Ca Al Fe2 Fe3
energygrp_table = O Al O Ca O Fe2 O Fe3 O Na O O O Si Si Al Si Ca Si Fe2 Si Fe3
Si Na Si Si Na Al Na Ca Na Fe2 Na Fe3 Na Na Ca Al Ca Ca Ca Fe2 Ca Fe3 Al Al Al
Fe2 Al Fe3 Fe2 Fe2 Fe2 Fe3 Fe3 Fe3
and in the .top file:
[ atomtypes ]
;name mass charge ptype A B
O 15.99940 -1.20000 A 0.0 0.0
Na 22.99000 0.60000 A 0.0 0.0
Si 28.08000 2.40000 A 0.0 0.0
Ca 40.07800 1.20000 A 0.0 0.0
Al 26.98200 1.80000 A 0.0 0.0
Fe2 55.30500 1.20000 A 0.0 0.0
Fe3 55.30500 1.80000 A 0.0 0.0
[ nonbond_params ]
; i j func C6 C12
O O 1 4.0904959800 2.12268E-09
O Si 1 32.858468400 9.64853E-11
O Na 1 2.2541869930 4.82427E-10
O Ca 1 2.9149186000 4.82427E-10
O Al 1 34.887265640 8.68368E-11
O Fe3 1 40.425524240 1.92800E-10
O Fe2 1 7.542 1.92800E-10
...
Also in the .top file, I define a moleculetype Fe, which is Fe2 in state A and
Fe3 in state B:
[ moleculetype ]
; name nrexcl
Fe 0
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 Fe2 1 Fe Fe 2 1.2 55.3050 Fe3 1.8 55.305
I expect that I could specify this atom in the gro file like this:
...
1764Na Na 1764 3.448 3.335 0.801 0.9202 0.1009 -0.6229
1765Fe Fe 1765 1.123 1.300 0.562 0.3254 -1.0409 -0.6704
1766Ca Ca 1766 2.536 3.320 1.379 -0.5737 -0.4492 -1.8149
...
The problem is that grompp fails, telling me
“
Fatal error:
Group Fe2 not found in indexfile
“
So, while I want to associate the tables with atom types, it seems GMX is
expecting that I am associating the tables (through the energy groups) with a
particular atom, which, in my case, moves between two atom types in the BAR
calculation.
Can anyone tell me whether I am just suffering from a misconception about how
the tables (or energy groups) are used, or whether it is in fact just not
possible to do BAR (or other free energy) calculations in this way?
Group names must be valid [moleculetype] names or whatever is listed in a
suitable index file. You've used the name Fe2 as a group, when in fact it is an
atom type. If you want to set this as an energygrp, then the appropriate name
is Fe, which is the name of the [moleculetype] shown in the topology above.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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