GROMACS version: 2022
GROMACS modification: No
Hi, folks!
I posted this question on MARTINI forum, but I did get no feedback yet. I’m running free energy of solvation of some Coarse-Grain (CG) molecules using Thermodynamic Integration (TI). After I ran the Bennet acceptance ratio I got only the histogram (as output) and the message “No results to calculate”. I don’t understand what’s happening. Have someone faced this kind of problem? I think my setup and protocol are fine.
Command: gmx bar -f dhdl*xvg -o -oi -oh -b 10000
Details: I’m using a soft-core potential (with ? of 0.5 and power set to 1). My systems were minimized and equilibrated for 50 ns. Each lambda point was run for 20 ns, but only the last 10 ns were used in gmx bar calculation (-b 10000). I’m using MARTINI 3 (FF), GROMACS 2022.0, 31 lambda points (first I decouple electrostatic and then van der Waals).
Thanks in advance,
Fred
Hi,
You could check that 1) the dhdl.xvg file contain the desired information 2) corresponds to different lambda values and 3) that the command read all the dhdl.xvg files. I guess from your command line that you have several dhdl.xvg file in the working directory.
Then you could have a look at the histograms. Do they have the expected trend?
\Alessandra
Dear Alessandra,
Thank you so much for your reply. I have been thinking about your questions.
- I think, my dhdl*.xvg files are fine, but I cannot see so much difference between them. In fact, when I run gmx bar I see on screen:
dhdl.22.xvg: Ignoring set ‘Total Energy (kJ/mol)’.
dhdl.22.xvg: Ignoring set ‘pV (kJ/mol)’.
dhdl.22.xvg: 0.0 - 20000.0; lambda = (0, 0, 0, 0, 0)
dH/dl & foreign lambdas:
dH/dl (mass-lambda) (100001 pts)
dH/dl (coul-lambda) (100001 pts)
dH/dl (vdw-lambda) (100001 pts)
dH/dl (bonded-lambda) (100001 pts)
dH/dl (restraint-lambda) (100001 pts)
delta H to (0, 0, 0, 0, 0) (100001 pts)
delta H to (0, 0.25, 0, 0, 0) (100001 pts)
dhdl.23.xvg: Ignoring set ‘Total Energy (kJ/mol)’.
dhdl.23.xvg: Ignoring set ‘pV (kJ/mol)’.
dhdl.23.xvg: 0.0 - 20000.0; lambda = (0, 0, 0, 0, 0)
dH/dl & foreign lambdas:
dH/dl (mass-lambda) (100001 pts)
dH/dl (coul-lambda) (100001 pts)
dH/dl (vdw-lambda) (100001 pts)
dH/dl (bonded-lambda) (100001 pts)
dH/dl (restraint-lambda) (100001 pts)
delta H to (0, 0, 0, 0, 0) (100001 pts)
delta H to (0, 0.25, 0, 0, 0) (100001 pts)
Samples in time interval: 0.000 - 20000.000
Removing samples outside of: 10000.000 - 20000.000
Does it look like both files have the same content? My histogram looks strange. I got a great number of points around 0, but also a histogram around 50.
Hi,
If all the xvg file looks similar, it could be that you forgot to change init-lambda-state in mdp to define the different lambdas.
\Alessandra
Hi! Thank you again. You’re right. I probably made a mistake in my submission script. It creates different directories for each lambda, but when I open the log files, all calculations were done for the same lambda.
Sorry for bothering you with my basic error.
Thanks.
