Dear Amber User:
I've been trying for several weeks to implement the Widom insertion method to obtain chemical potential and also Henry constant of solutes method using amber.Basically what I do is to generate a enough configurations of a waterbox, running a MD ,let's say for 1ns, and then I insert a particle of a noble gas (Ar) in the box and I recalculate the potential energy for that configuration running a very short MD in order to avoid relaxation of the system.I've check all the parameter for the water, the Argon and the water-argon interaction. I'm using SPCE model for water.My problem is the the box seem to have a unusual number of cavities so that in the end The Henry constant is much smaller that what it should be comparing whit previous works.My question is Has anyone used the Widom insertion method with amber an have some advice for me or has encouter the same problems as I ??
I give the L-J parameters that I'm using as are written in the top file
A coefficients for Ar ; Ar-H2O ; H2O2.49574476E+06 1.26413119E+06 6.29362166E+05
B coefficients for Ar ; Ar-H2O ; H2O1.57346077E+03 9.96166345E+02 6.25267765E+02
I olso give the input for the Energy calculation if the box with the solute &cntrl imin=0,irest=0,ntx=1,
ntb=2,ntp=1,
NSTLIM= 1, DT=.000000001, NTC=2,NTF=2,nrespa=1,
ntt=1,tempi=200.0,temp0=300.0, tautp=0.000000001, taup=99999999999999999999, ntpr=1,ntwx=1,ntwv=0,ntwe=1, iwrap=1,
cut = 8.0
&end
Note that the timestep is very short in order to avoid relaxation of the sistem.Olso I need to work at NVT and measure the pressure so I put ntb=2 and ntp=1, but a very large taup
Thanks for any help you can provide
Matias.F
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Received on Tue Aug 16 2011 - 12:30:02 PDT
