[gmx-users] problem with git/4.6

Michael Brunsteiner mbx0009 at yahoo.com
Fri Jun 29 17:08:05 CEST 2012

> You should have it.  In CMakeLists.txt, PROJECT_VERSION should be set to 
> "4.6-dev" so you can check that.

ithat what i looks like ... i now get:

prompt> mdrun_d
:-)  VERSION 4.6-dev-20120629-9c6be1c  (-:

which gives me:
g_bar_d -f mdv*.xvg -b 100
total   0.000 -  1.000,   DG -9.00 +/-  0.15

with vanilla 4.5.5 i get:
g_bar_d -f mdv*.xvg -b 100
total   0.000 -  1.000,   DG -9.00 +/-  0.15

there's two points:

1) this value is fine, as, once combined with the coulomb part, it is very close to literature and
exptl data. however, in both cases  get this warning ...  Second Law of Thermodynamics etc...
and riduculously high s_B values at lambda=0.

2) the reason i saw different DeltaG values earlier was that i had included (by mistake)
the dhdl file from a single additional window at lambda=0 that was produced with exactly the same
input apart from the value of 0.3 (instead of 0.5) for sc_sigma ... as far as i understand things (not very
well perhaps) the resulting free energy difference should NOT depend on this parameter ... so neither should
the result of g_bar ... but maybe it does when using foreign lambdas as i did here ? if this is so
it might be a good idea making g_bar read tpr files to give a warning in such a case ...

i guess for now i'll wait for a stable 4.6 - any ideas when this will be there?


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