GROMACS version:2023
GROMACS modification: Yes
Greetings to you all
I have run a REMD simulation with the following details:
- dodecahedral box with -d 1 spacing
- 14 temperatures each one run for 10 ns.
- System equilibrated with nvt > npt and run with npt (C-rescale)
- Exchange probability 0.2 (Temperature generator for REMD-simulations)
When I look for the average probabilities over the replica I obtain the following:
RUN310.00/remd.log:Repl average probabilities:
RUN310.00/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN310.00/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN310.00/remd.log-Repl number of exchanges:
RUN310.00/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN310.00/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN310.00/remd.log-Repl average number of exchanges:
RUN310.00/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN310.00/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN310.00/remd.log-
RUN311.67/remd.log:Repl average probabilities:
RUN311.67/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN311.67/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN311.67/remd.log-Repl number of exchanges:
RUN311.67/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN311.67/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN311.67/remd.log-Repl average number of exchanges:
RUN311.67/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN311.67/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN311.67/remd.log-
RUN313.36/remd.log:Repl average probabilities:
RUN313.36/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN313.36/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN313.36/remd.log-Repl number of exchanges:
RUN313.36/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN313.36/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN313.36/remd.log-Repl average number of exchanges:
RUN313.36/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN313.36/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN313.36/remd.log-
RUN315.04/remd.log:Repl average probabilities:
RUN315.04/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN315.04/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN315.04/remd.log-Repl number of exchanges:
RUN315.04/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN315.04/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN315.04/remd.log-Repl average number of exchanges:
RUN315.04/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN315.04/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN315.04/remd.log-
RUN316.74/remd.log:Repl average probabilities:
RUN316.74/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN316.74/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN316.74/remd.log-Repl number of exchanges:
RUN316.74/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN316.74/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN316.74/remd.log-Repl average number of exchanges:
RUN316.74/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN316.74/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN316.74/remd.log-
RUN318.44/remd.log:Repl average probabilities:
RUN318.44/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN318.44/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN318.44/remd.log-Repl number of exchanges:
RUN318.44/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN318.44/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN318.44/remd.log-Repl average number of exchanges:
RUN318.44/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN318.44/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN318.44/remd.log-
RUN320.15/remd.log:Repl average probabilities:
RUN320.15/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN320.15/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN320.15/remd.log-Repl number of exchanges:
RUN320.15/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN320.15/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN320.15/remd.log-Repl average number of exchanges:
RUN320.15/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN320.15/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN320.15/remd.log-
RUN321.86/remd.log:Repl average probabilities:
RUN321.86/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN321.86/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN321.86/remd.log-Repl number of exchanges:
RUN321.86/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN321.86/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN321.86/remd.log-Repl average number of exchanges:
RUN321.86/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN321.86/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN321.86/remd.log-
RUN323.59/remd.log:Repl average probabilities:
RUN323.59/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN323.59/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN323.59/remd.log-Repl number of exchanges:
RUN323.59/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN323.59/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN323.59/remd.log-Repl average number of exchanges:
RUN323.59/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN323.59/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN323.59/remd.log-
RUN325.32/remd.log:Repl average probabilities:
RUN325.32/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN325.32/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN325.32/remd.log-Repl number of exchanges:
RUN325.32/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN325.32/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN325.32/remd.log-Repl average number of exchanges:
RUN325.32/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN325.32/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN325.32/remd.log-
RUN327.05/remd.log:Repl average probabilities:
RUN327.05/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN327.05/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN327.05/remd.log-Repl number of exchanges:
RUN327.05/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN327.05/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN327.05/remd.log-Repl average number of exchanges:
RUN327.05/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN327.05/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN327.05/remd.log-
RUN328.80/remd.log:Repl average probabilities:
RUN328.80/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN328.80/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN328.80/remd.log-Repl number of exchanges:
RUN328.80/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN328.80/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN328.80/remd.log-Repl average number of exchanges:
RUN328.80/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN328.80/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN328.80/remd.log-
RUN330.55/remd.log:Repl average probabilities:
RUN330.55/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN330.55/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN330.55/remd.log-Repl number of exchanges:
RUN330.55/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN330.55/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN330.55/remd.log-Repl average number of exchanges:
RUN330.55/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN330.55/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN330.55/remd.log-
RUN331.00/remd.log:Repl average probabilities:
RUN331.00/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN331.00/remd.log-Repl .27 .33 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN331.00/remd.log-Repl number of exchanges:
RUN331.00/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN331.00/remd.log-Repl 6611 8113 8982 8195 8945 9157 8332 8270 8920 9190 8401 8760 19631
RUN331.00/remd.log-Repl average number of exchanges:
RUN331.00/remd.log-Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 13
RUN331.00/remd.log-Repl .26 .32 .36 .33 .36 .37 .33 .33 .36 .37 .34 .35 .79
RUN331.00/remd.log-
with the minimum being 0.27 and the maximum 0.79. Must the value be 0.2 everywhere or is it acceptable as is?
When I check for the actual exchange (see file “exchange”) it seems the replica communicate a lot between one another and the potential distributions seem to overlap nicely (see file “probability-distribution-normalized”). However, in the last one the last four temperature do not feature a complete gaussian trend. Why is that so?
In the end, based also on what I had red from previous discussions, I would like to know if my exchange rate is ok.
Thank you all for any comments and suggestions.
Valerio
