Moeed wrote:
Hi Justin,
I was looking all the time for a file with dgdl extension throughout the
directory. IIRC in previous versions -dgdl would generate such
extension. I found now .xvg file which has dhdl data. (if I am right
dgdl is the very dhdl in 4.5.3!)
The extension has always been .xvg, but the root filename has changed. It is
now perhaps a bit more accurate (delta Hamiltonian).
I have a little problem with FE output file. Below is the
settings and also I am including -dgdl in the command I issue
but no dgdl (or dhdl) file generates. I dont figure where the
problem lies ! (version 4.5.3).
How long has the simulation been running? Output is buffered, and I
find that dhdl.xvg is not updated often.
free_energy = yes
init_lambda = 0 delta_lambda = 0
sc_alpha = 0.5
sc-power = 1
sc_sigma = 0.3
foreign_lambda = 0.1
dhdl_derivatives = yes
couple-moltype = Polymer
couple-lambda0 = vdw-q couple-lambda1 = none
Note that turning off all interactions simultaneously (especially
when using soft-core) can be very unstable. You should (de)couple
vdW and Coulombic interactions separately.
Yes I read your comment about decoupling separately earlier on but I was
not sure if this could depend upon the system so I was thinking of
comparing results from two trials:
trial 1:
couple-lambda0 = vdw-q
couple-lambda1 = none
trail 2 A:
couple-lambda0 = vdw-q
couple-lambda1 = vdw
trail 2 B
couple-lambda0 = vdw
couple-lambda1 = none
So:
1- Does this decoupling issue depend on the system or it is a must for
all FE studies?
No, it pertains to the very stability of all calculations. Whenever I've
decoupled charges and LJ simultaneously, either the simulations crash or the
resulting energies are not reliable. There are numerous book chapters and
papers dedicated to these topics.
2- I actually went through many of FE posts and never found how separete
decoupling can be done. from trail 2 A and B I get dgdl files but how
to get total vdw-q to none from these two? Please shed some light on the
details of procedure..
Add them. DeltaG is a state function.
3- With free_energy turned off my runs take only a few hours but as I
shift to free_energy = yes, runs take nearly one day foe each
lambda.. Is this normal for s system having 2500 atoms?
Yes. The free energy code slows down runs quite a bit.
-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
========================================
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