down/ and up/ directories

[ghost]

Hey!

I divided my membrane into 60 bins and after I run umbrella sampling simulations using Gromacs, I have 60 different umbrella{i}_pullf.xvg and umbrella{i}_pullx.xvg (i= 0 to 50) files. Do I need to put these files in two down/ and up/ directories and then run the setup.sh and getDall.py to get the diffusion curve? Actually I did and the result(attached photo) was nonsense.

I would be appreciated if you can advise me to fix it.

[cnrowley]

How frequently are you saving your steps from your simulation? For diffusion, you usually have to save them at every step.

On Tue, Sep 15, 2020 at 7:45 AM Javad notifications@github.com wrote:

Hey!

I divided my membrane into 60 bins and after I run umbrella sampling simulations, I have 6 [image: Screenshot 2020-09-15 at 6 15 12 PM] https://user-images.githubusercontent.com/42797415/93198308-6d9af300-f77f-11ea-92c4-952ffeecf3c3.png 0 different umbrella{i}_pullf.xvg and umbrella{i}_pullx.xvg (i= 0 to 50) files. Do I need to put these files in two down/ and up/ directories and then run the setup.sh and getDall.py to get the diffusion curve? Actually I did and the result(attached photo) was nonsense.

I would be appreciated if you can advise me to fix it.

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[ghost]

Thanks for your reply.

I just set -s value to 2 as it was in the original script. I have run every bin of membrane for 50 ns so it means I should set the value of s to 25000000? Also, do you know what's the optimum value for --maxcorr ? it looks changing its value, doesn't change the curve for my simulation

[cnrowley]

No, how often are you saving the position of the solute in your MD simulation?

On Tue, Sep 15, 2020 at 12:02 PM Javad notifications@github.com wrote:

Thanks for your reply.

Do you mean --maxcorr value? I set it 10000 in setup.sh script. Also, I have run every bin of membrane for 50 ns.

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[ghost]

I have set nstxout-compressed = 500 in my simulation which is 50ns run time for every bin (60 bins in total). Can you advise me on how I should set the input values to get the right diffusion curve?

Based on my understanding, I should set -f value to 1 as I used Gromacs, -s value to 2000 as every step in my simulation is 2 ps which is 2000 fs and --maxcorr to 50000 , but I face below error for every bin:

Time step of 2000 fs will be used.

No cutoff will be used to integrate the ACF.

D(s) will be saved in out_up_sim_2.out

var 1.15969e+10

varVel 6.54981e-30

WARNING: ACF has only decayed to 94.4956% of initial value at the end of the region of integration.

libc++abi.dylib: terminating with uncaught exception of type boost::wrapexcept: Error in function boost::math::tools::toms748_solve: Parameters a and b do not bracket the root: a=9.9999999999999995e-07 setup.sh: line 6: 34857 Abort trap: 6 /Users/javad/Downloads/ACFCalculator-master/build/ACFcalculator -i umbrella${i}_pullx.xvg -t gromacs -a acf_upsim${i}.dat -o out_upsim${i}.out -f 1 -s 2000 --maxcorr 50000

[cnrowley]

This is a somewhat different issue. You have to save a time series for the coordinate you are calculating the diffusion coefficient for at every step. I would recommend reading the paper https://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00747 carefully before attempting to do these calculations.

On Wed, Sep 16, 2020 at 12:48 AM Javad notifications@github.com wrote:

I have set nstxout-compressed = 500 in my simulation.

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