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    Mohammad Soroush Barhaghi
    @msoroush
    What is happening is that the code stuck in infinite while loop because it cannot find a bond with pair atom between 1 and 849.
    Tom-Pope
    @Tom-Pope
    ahh okay
    will do, thanks for the help
    Mohammad Soroush Barhaghi
    @msoroush
    I will let you know once I found better algorithm to solve this issue
    Mohammad Soroush Barhaghi
    @msoroush
    @Tom-Pope would you please use the development branch? I pushed the fix in the development branch. Please check the defined bonded parameters in console file (log file) and let me know if there is any problem.
    Tom-Pope
    @Tom-Pope
    @msoroush I will do this thank you --- I was also wondering if the simulation cpu time/wallclock time printed at the end of the restarted simulation with reflect the entire simulation time (pre-restart + restarted simulation) or if it will just print the time of the restarted simulation. Time benchmarking is important to me at the moment and due to the complexity of my simulations the time produced per step in the console file fluctuates considerably and hence can't be used as a legitimate benchmark
    Mohammad Soroush Barhaghi
    @msoroush
    @Tom-Pope The total simulation time that we print at the end is wall-clock and it only reflects the simulation time from step 0. It doesn’t consider the initialization or reading of the file that gomc does before starting the simulation. If you need to calculate the total cpu hours, just multiple the the time by number of CPUs.
    Mohammad Soroush Barhaghi
    @msoroush
    @Tom-Pope I was looking at your config file for IBA adsorption in OREVQ and I though I can give you some tip on your system.
    Tom-Pope
    @Tom-Pope
    @msoroush sounds good, what do you think?
    Mohammad Soroush Barhaghi
    @msoroush
    1- You can use RcutLow 1.0 to reject any move that puts any atom closer than 1 A distance from other molecules. This would also help to increase the code performance by avoiding reciprocal energy calculation. It would also prevent atom collapse for naked charge atom (no LJ interaction, e.g. hydrogens).
    Tom-Pope
    @Tom-Pope
    ahh okay, thanks for the tip
    Mohammad Soroush Barhaghi
    @msoroush
    2- Any Monte Carlo moves that involves CBMC (e.g. regrowth, swap, intra-swap), depend on CBMC parameters become very expensive. To avoid that, you can disable the intra-swap move IntraSwapFreq 0.0. In addition, since ibuprofen is relatively large compare to void area in your system, it would more beneficial to use more swap moves.
    3- For the same reason I explained in number 2, you could see improvement in molecule swap move by increasing the CBMC trial for first atom CBMC_First 16 and decreasing the CBMC trials for secondary atoms CBMC_Nth 5. You could potentially do a benchmark to see which set of parameter would give you higher acceptance, or efficiency (accepted/CPU-time). Unfortunately the CBMC parameters is unique for each system, but you will get the general rule of thumb after few trials.
    Tom-Pope
    @Tom-Pope
    awesome, thanks for the help!
    Mohammad Soroush Barhaghi
    @msoroush
    4- When I tried to visualize the GOMC output in VMD, I noticed that the adsorbent is shifted relative to the defined box. This is due to unwrapping operation GOMC does before printing the coordinates. Since the adsorbent is a huge molecule, when you unwrap it around its centroid, you will get this representation.
    Tom-Pope
    @Tom-Pope
    aah yes I have been meaning to ask you about that
    do you know of an easy to fix this possibly in vmd, rather than playing with the coordinates to translate both boxes into the sam frame of reference
    Mohammad Soroush Barhaghi
    @msoroush
    Any analysis tools in VMD supports wrapping. When you wrap all the molecules in the system, you get some ugly picture and it is necessary for accurate analysis.
    The work around that is as follow:
    1- load your psf and pdb file in vmd: vmd OUTPUT_merged.psb OUTPUT_BOX_0.pdb
    2- Open the TkConsole in vmd. Tu visualize the box, execute this command in TkConsole: pbc box or pbc box -color 4
    You will see how the adsorbent molecules are shifted.
    3- To only wrap the adsorbent molecule (PEVQ), execute this command in TkConsole: pbc wrap -sel "resname PEVQ"
    Mohammad Soroush Barhaghi
    @msoroush
    This would only apply the wrapping operation on our selection, which is "resname PEVQ". Now you can see nice looking image.
    4- If you want to do the same for all frames, execute this: pbc wrap -sel "resname PEVQ" -all
    5- If you want to wrap all the molecules, including the adsorbate, for all the frames, execute this pbc wrap -all
    Here is the link to VMD PBC plugin to learn more about pbc functionality.
    Please let me know if you have any other question.
    Tom-Pope
    @Tom-Pope
    okay thank you very much for the help
    Mohammad Soroush Barhaghi
    @msoroush
    No problem.
    Mohammad Soroush Barhaghi
    @msoroush
    @Tom-Pope I saw you are using all atom ibuprofen. If you are using OPLS model, they are using different combining rules (geometric mean for sigma). In GOMC to activate this option, you need to set VDWGeometricSigma true. In addition, you might need to use Exclude 1-3 to consider 1-4 and 1-n interaction in sampling geometric of your molecule.
    Tom-Pope
    @Tom-Pope
    ah okay I wasn't aware of that thanks
    Tom-Pope
    @Tom-Pope
    @msoroush I've run into another problem, I'm trying to set up some aspirin simulations as well and I'm running into the same error every time. "Printed combined psf to file ASP_EDUSIF_1.00_merged.psf
    Error: Cannot Construct Angle CB CB CB !". I've generated the pdb and top file from molefracture with care and the pdb should correspond to the correct angles --- these angles are also defined in the force field file. which leads me to believe it is a problem with the CBMC for this particular adsorbate. I've fiddled with the cbmc scheme parameters to see if I could get around the issue but I have failed to. Do you have any insight on this issue?
    Tom-Pope
    @Tom-Pope
    I've run into the same problem with the recalculate procedure as with the restart procedure before
    when attempting to recalculate each snap shot GOMC gets stuck in an infinite loop and hangs just after the coordinates have been read in
    Tom-Pope
    @Tom-Pope
    my mistake sorry --- I was using an old version of the executable
    Mohammad Soroush Barhaghi
    @msoroush
    @Tom-Pope no worries. Let me look into your system and I will get back to you. This error message usually related to CBMC algorithm to construct angles at branching point. When someone tries to fix specific angles and flexing the rest, it becomes impossible to generate such a structure
    Tom-Pope
    @Tom-Pope
    also I there is another error being generated in my Ibuprofen simulations: 'Wrapping molecules inside the simulation box 1:
    Error: Multiple atoms with zero coordinates were found'
    if you could let me know the common cause for this error I will trouble shoot it myself
    Mohammad Soroush Barhaghi
    @msoroush

    @Tom-Pope I looked at your system, and I believe the problem is in the parameter file.
    This problem only happens when you are trying to construct a branching point that forms a plane and this a due to mathematical limitation.
    Let's focus on the oxygen atom attached to the benzene ring in aspirin molecule. In your parameter file we have:

    Angles parameter:
    Atom Types                         Ktheta(K)         theta0(degree) 
    OR    CB    CB                      35056.0000         120.0000
    CB    CB    CB                      24227.6600         119.9770

    We have one OR-CB-CB and two CB-CB-CB angles at this branching point.
    Having 3 angles with equilibrium value near 120, it means they must be in the same plane. When you have flexible angles, if you pick an angle above 120 (let's say OR-CB-CB angle is 122), it means that sum of the both CB-CB-CB angles must be less than 238, otherwise you cannot construct such a geometry. If in your trial angle generation, you try angles with summation above 238, you will get this error message.
    To solve your problem, I would suggest to fix the angles for OR-CB-CB, CB-CB-CB, CB-CB-HCMM. Its very important to make sure when you build your molecule, the CB-CB-CB, CB-CB-HCMM angles are exactly 120. Otherwise we would get the same error. Until we find another way around to solve this problem.

    also I there is another error being generated in my Ibuprofen simulations: 'Wrapping molecules inside the simulation box 1:
    Error: Multiple atoms with zero coordinates were found'

    Please check you PDB file for simulation box 1. Sometimes packing or PSF generation failed which results in generating zero value for X, Y, and Z coordinates. If you found multiple molecules with zero coordinate, it means PSF generation failed due to possible mistake in topology file. You can look into the warning generated from vmd.

    Tom-Pope
    @Tom-Pope
    thank you very much --- got my aspirin simulations up and running and I'm sure I will find the error in the topology for ibuprofen when I get round to it
    Tom-Pope
    @Tom-Pope
    Hi I've noticed during restarting simulations that the total energy of the system is lower in magnitude post restart to the pre-restarted simulation, I've checked the contributions and the electrostatic energy reduces in magnitude by 1e+05 (for my particular case). I boiled it down to the contribution form the self interaction and correction electrostatic energies --- it seems to me that the self interactions and correction electrostatics of the framework (box0) is recomputed when a simulation is restarted with adsorbates already in the box 0 containing the framework (taken from the restart coordinate files) --- would it be possible to add in a flag to the configure file that allows you to use the pre restarted self interaction and correction to allow for simulation continuity --- this would be a very helpful feature for my style of research where adsorbate-adsorbent interactions are a main goal and simulations will have to be restarted a lot due to the size of the guests
    Mohammad Soroush Barhaghi
    @msoroush
    @Tom-Pope since there are multiple ways to define adsorbent structures, it would be very difficult to detect it and exclude it from simulation interactions. Can you use simulation box with no adsorbate, to calculate the energy associated with framework and subtract this energy from your restart or recalculated energy?
    Tom-Pope
    @Tom-Pope
    Hi, yes that's what I've been doing I just thought it might be a good idea in aid of high throughput but it's not a tough task to automate for many structures
    cheers
    Tom-Pope
    @Tom-Pope
    I have a query about dihedrals terms --- if I wan't to use a mixture of TraPPE style dihedrals, CFF dihedrals and three cosine dihedrals, is it valid to use these in GOMC converting to the charmm style format? also for the reference angles needed by charmm do I choose either 180 or 0 for dihedral forms that do not provide reference angles based on the configuration of my molecule?
    Mohammad Soroush Barhaghi
    @msoroush
    Hi @Tom-Pope. Please mention me in your text, so I get the notification. Regarding your question, TraPPE sometimes uses non standard form of dihedral as you may saw. The best and the safest method is to try to refit the TraPPE dihedral energy to Charmm style dihedral, no matter what phase shift value (0, 180) you use. This is valid as long as you reproduce the same dihedral energy as the function phi, no matter what equation form you are using.
    Tom-Pope
    @Tom-Pope
    @msoroush ah okay thank you