On 6/18/12 10:41 AM, Daniel wrote:
Hi everyone,
I'm having problems when calculating Free energy through the g_bar tool. I'm
trying to decouple separately the electrostatic and the Vdw terms. So, after
performing the mdruns for all Coulombic processes (from 0 to 1, split in 0.1
steps: 0.0-0.1-
Hi everyone,
I'm having problems when calculating Free energy through the g_bar tool. I'm
trying to decouple separately the electrostatic and the Vdw terms. So, after
performing the mdruns for all Coulombic processes (from 0 to 1, split in 0.1
steps: 0.0-0.1-0.2...0.9-1.0) and the same for the LJ-
Dear Emanuel:
We need you to be much more specific.
1. What link?
2. Even though it might be in the link, you should still provide us
with a general protocol that you followed.
Chris.
-- original message --
I am using Gromacs to calculate solvation of free energy calculation.
First I tri
Hi
I am using Gromacs to calculate solvation of free energy calculation. First I
tried the tutorial I found on the following link and run all the simulations
for different lambda values 36 run for both in water and in vacuum and I got
25215.67 is gromacs calculate this in J or KJ? Even if it i
Paolo,
As for the LJ decoupling,I cannot obtain a smooth curve and dG/dlambda
has large deviations even if I use sc_alpha = 0.5 and sc_power = 1 as
suggested by Shirts.
This doesn't typically give a smooth curve in the sense of
featureless, like the electrostatics curve. However, the particula
Dear all,
I'm trying to calculate solvation free energy for an ALANINE molecule in
water with the usual method: I calculate dG/dlambda for different values
of lambda and then integrate.
I start with my molecule fully interacting with solvent (water SPC) and
then decouple the solute-solvent Coulomb
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