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274 discussions

Monte carlo temperature in ReplicaExchange0
by Genis Valentin 17 Oct '18

17 Oct '18

Hello everyone I am modeling a system with the ReplicaExchange0 macro and my simulation constantly falls into a local energy minima after a few replica exchange steps (<100). This reduces a lot the reproducibility of the simulation, as the final results greatly depend on the starting configuration of the rigid bodies. I realized that tweaking temperature parameters improves the situation, which allows the simulation to sample a much larger space and hopefully explore all minima. I would like to know if the values that I chose in the following parameters are in reasonable range. monte_carlo_temperature = 100 replica_exchange_minimum_temperature = 100 replica_exchange_maximum_temperature = 250 Thank you and best regards Genis Valentin

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Waiting for your response
by mariam ahmed 17 Jul '18

17 Jul '18

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IMP 2.9.0 release
by Ben Webb 03 Jul '18

03 Jul '18

IMP 2.9.0 is now available. This is a bugfix and major update release. Most notably a number of new applications of IMP are now available, including the elucidation of the structure of the entire yeast nuclear pore complex. This release also includes a number of bug fixes and performance improvements. See https://integrativemodeling.org/2.9.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Correctly setting non-default temperatures in Brownian dynamics simulations
by Barak Raveh 02 Jul '18

02 Jul '18

This note is for advanced BD (and possibly MD) users only - it is not relevant if you simulate IMP at the default IMP temperature (297.15 K). The issue if you do simulations at non-default temperature is that the particles diffusion coefficients scale with T according to the equations of Brownian However, The BrownianDynamics class relies on whatever diffusion coefficients were set by the Diffusion decorator, regardless of the simulation temperature. Therefore, to simulate correctly at non-default temperatures, one must do two things: (1) Call BrownianDynamics::set_temperature() (2) Update the diffusion coefficients for all particles to scale with temperature - e.g. D is 10% higher at 330 K than at 300 K. I will update the IMP documentation to explain this subtlety. Let me know if you think we should change the code behavior. Perhaps we can add code to automatically update D, but it's also risky and could lead to unexpected behavior. Barak

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Defining Possible Interactions
by Komjati Kornel 07 Jun '18

07 Jun '18

Hi all, I am trying to create a protein network which is able to reorganize itself upon environment/parameter changes. I have several components that can interact with spatially separated domains but I found the Crosslink Restraint not suitable to define this. Whenever a domain has multiple crosslinks given to it, in the minimal output the domain is always equally far from its interaction sites. Is it possible to have all the possible interactions as input, but the domain chooses only one of them (the optimal one depending on the spatial configuration)? Maybe a logarithmic approach for converging to one of them or using a different restraint. (I am using the BuildModel macro.) Thanks in advance, Komjati Kornel

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ExcludedVolumeSphere resolution
by Julian 22 May '18

22 May '18

Dear IMP, I was wondering if the resolution parameter in IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere should depend on the scale of the model. In most scripts I've seen on github, the resolution is set to 10. But I was thinking if Beadsize is 50 or 100, maybe it would make more sense to increase this parameter? Thanks much, Julian

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Rigid body from multiple chains
by Komjati Kornel 26 Feb '18

26 Feb '18

Hi, I would like to model a protein with multiple chains (A,B,C,D) as an entire rigid body. Unfortunately I cannot find a way to do this, it seems like that a rigid body can only contain one protein chain. Is there any method to create my desired model? Thanks in advance, Kornel

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running imp with DNA sequence
by מירב בריטברד 05 Feb '18

05 Feb '18

Hi, Part of the structure that I am trying to find is a DNA sequence and not a protein. I have pdb with the DNA part, and I create a fasta file (both attached) but when I am running IMP, it's write this warning: "BuildSystem.add_state: -------- domain 0 of molecule DNA_1 represented by pdb file /cs/labs/dina/meravb/CENP_new_cross_links_and_PDB_renumbered/pdb_files/Nuc_numbering_fixed_in_map.pdb WARNING: Replacing sequence residue 1 "THR" with PDB type "DC" WARNING: Replacing sequence residue 2 "GLY" with PDB type "DT" WARNING: Replacing sequence residue 3 "CYS" with PDB type "DG" WARNING: Replacing sequence residue 4 "ALA" with PDB type "DC" WARNING: Replacing sequence residue 5 "GLY" with PDB type "DA" WARNING: Replacing sequence residue 6 "ALA" with PDB type "DG" WARNING: Replacing sequence residue 7 "THR" with PDB type "DA" WARNING: Replacing sequence residue 8 "THR" with PDB type "DT" WARNING: Replacing sequence residue 9 "CYS" with PDB type "DT"....." How can I run in imp in a way that will recognize the DNA? Thanks, Merav

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IMP: moving a gaussian decorated flexible bead
by Fergal Duffy 30 Jan '18

30 Jan '18

Hi, I have noticed an odd thing when trying to shuffle flexible beads decorated with Gaussian particles. The code in IMP.pmi.tools.shuffle_configuration uses xyz=[fb.get_value(IMP.FloatKey(4)), fb.get_value(IMP.FloatKey(5)), fb.get_value(IMP.FloatKey(6))] to get the initial XYZ location of the Gaussian fb. However, this location does not return the same value as IMP.core.XYZ(fb) And it looks like IMP.core.XYZ is actually the correct location of the floppy body, leading to some odd results when shuffling based on the fb.get_value() based locations. What is the correct way to find the location of, and move, a Gaussian decorated flexible bead? Fergal Duffy Staff Scientist Center for Infectious Disease Research<http://www.cidresearch.org/> 307 Westlake Ave N, Suite 500 | Seattle, WA 98109 206.256.7435 | fergal.duffy(a)cidresearch.org<mailto:fergal.duffy@cidresearch.org>

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a problem with the updated IMP
by מירב בריטברד 16 Jan '18

16 Jan '18

I install an updated IMP on my computer and try to run the modeling.py script. But when I try to open the rmf file from this run in chimera I got this message: [image: Inline image 2] What can I do in order to open the rmf file and work as usual? Thanks, Merav

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