[gmx-users] Umbrella Sampling - Experiment Question
Hi there, I'm thinking about running an Umbrella sampling of a protein and before I start spending a ton of time on running/figuring out how to run the simulations I was wondering if I could get some feedback on my experimental design aka I want to find out if what I want to do makes sense. Basic setup is this; I have an ~350 amino acid protein that contains a distinct N and a distinct C terminal lobe connected by a large beta sheet between each lobe. Although the protein is a whole singular unit naming convention and the morphology/structure of the protein provide a clear center point to pull from in the beta sheet connecting them. We know from wet lab experiments that one lobe is far less stable than the other so in order to try and find out why I've generated a series of mutants in the wet lab for the unstable lobe only and I am currently testing said mutants using chemical unfolding experiments to try and determine if the mutants have increased or decreased the stability of the enzyme. I have run previous experiments using standard MD simulations to try and simulate the unfolding but I have to have my protein unfold at high temperature or in a timely manner (over 100ns) and in a fashion that makes sense/matches the wet lab data. Unfortunately I do not have a ny structural information on the denatured states only the initial state. I have checked the energy, pressure, and temperature equilibration steps and yes they are all in acceptable limits and do come to stable baseline. Okay so to my actual questions! If I conduct an Umbrella experiment for my control protein and my mutants in which I pull at the COM as defined as the midpoint between the N and C terminal lobes can I utilize the PMF difference between the mutant and control to examine any increases or decreases in protein stability due to the mutation. Aka I'm hoping I can use umbrella sampling as a corollary to my unfolding experiments and if so does anyone have any tips/advice they can throw my way! If not are there any suggestions on things I should be looking into? Thanks so much for your help and sorry for asking a vague question as I don't have too many local resources to turn to for modelling help. Cheers, -Doug Grahame --- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Computing Resource - Laptop
Sorry I meant desktop, laptop must have been a mental error as I'm looking for a new personal laptop. -Douglas Grahame -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Szilárd Páll Sent: February 24, 2015 3:20 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Computing Resource - Laptop Did you mean laptop, desktop or both? I To be honest, would not use laptops for anything but lightweight analysis tasks. -- Szilárd On Tue, Feb 24, 2015 at 6:10 PM, Douglas Grahame dgrah...@uoguelph.ca wrote: Hey everyone I'm not sure if this is the place to post this or not so my apologies if it is not. Our lab recently got some funds to put towards a desktop for molecular dynamics work and we have a budget of aprx. $4,000 CDN for the laptop. Given that I am not an expert in the hardware area, nor do I have a ton in the simulation area either, I wanted to see if there was any suggestions or resources or even experiences that this mailing list may have so that we can get the most out of our money. Primarily the computer will be used to run GROMACS and be used for analysis and some small scale simulation work. We do have access to supercomputing clusters which will serve as the primary resource for modelling. Thanks for your help in advance! -Douglas Grahame --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Computing Resource - Laptop
Hey everyone I'm not sure if this is the place to post this or not so my apologies if it is not. Our lab recently got some funds to put towards a desktop for molecular dynamics work and we have a budget of aprx. $4,000 CDN for the laptop. Given that I am not an expert in the hardware area, nor do I have a ton in the simulation area either, I wanted to see if there was any suggestions or resources or even experiences that this mailing list may have so that we can get the most out of our money. Primarily the computer will be used to run GROMACS and be used for analysis and some small scale simulation work. We do have access to supercomputing clusters which will serve as the primary resource for modelling. Thanks for your help in advance! -Douglas Grahame --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Urea induced denaturation
Hi everyone, just wondering if anyone can suggest some papers or links to sources for urea induced denaturation. I'm trying to look at protein stability of various mutants but simulated annealing and simulations at constant temperature up to 500 ps haven't shown or reflected or wet lab data. Hoping to examine urea denaturation to assess the strength of a beta-barrel hydrophobic core. Any suggestions or hints in the right direction would be great! Thanks everyone, -Douglas Grahame BSc. MSc. PhD. Candidate dgrah...@uoguelph.ca --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Urea induced denaturation
Thanks Justin, pervious experiments were not with Urea but I'll try extending the simulation time further to 10 - 20ns and hopefully that will do it re: seeing denaturation. Thanks again, -Douglas Grahame BSc. MSc. PhD. Candidate dgrah...@uoguelph.ca -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: July 23, 2014 6:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Urea induced denaturation On 7/23/14, 6:46 PM, Douglas Grahame wrote: Hi everyone, just wondering if anyone can suggest some papers or links to sources for urea induced denaturation. I'm trying to look at protein stability of various mutants but simulated annealing and simulations at constant temperature up to 500 ps haven't shown or reflected or wet lab data. Hoping to examine urea denaturation to assess the strength of a beta-barrel hydrophobic core. Any suggestions or hints in the right direction would be great! Thanks everyone, 500 ps is not nearly enough time to see anything relevant happening, independent of whatever conditions you're using. The effects of simple thermal denaturation should be evident even within 10-20 ns, but everything you see is also a function of the force field and the quality of the urea parameters. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] simulation at acid medium
Hi Chris, I'm not sure if this is what you need specifically but I've been looking at protein denaturation in acidic and alkaline medium and the strategy that I've come up with is to generate a pdb file with the correct protonation state using this online tool (http://biophysics.cs.vt.edu/). From there I've been running a 'standard' simulation for 50 - 100ps using the amber99sbnmr1-ildn force field. Although the choice of force field is application specific and the time should be tailored to your project specifically as well I'm hoping that this gives me an appropriate data set to look at structural changes. Although this doesn't take into account an acidic medium it should still hopefully provide structural data, I've also been looking into constant pH simulations or trying to play around with the H++ concentration in the medium but I've been running into more challenges than I expected. To be honest not entirely sure if this is the best means of going about it either so if anyone else has any suggestions or alternative I'd love to hear them as well! Cheers and hope that helps, -Douglas Grahame BSc. MSc. PhD. Candidate dgrah...@uoguelph.ca -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of do...@iflysib.unlp.edu.ar Sent: July 7, 2014 10:46 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] simulation at acid medium Hi Erik Thanks for your hints Sorry, I have problems with internet, so I could not answer you before I thought something was wrong with the MD simulation at physiological solution since it looks like as a MD simulation at water. But I did not take into account the protonation states!!! Please, do you Know any another form to have acid medium?. thanks again, Chris Erik Marklund erik.markl...@chem.ox.ac.uk ha escrito: Then you essentially need to protonate the side chains according to their pKa and the pH. Note that the protons will not hop around between groups in normal MD. What makes you think something's wrong with your physiological solution? Kind regards, Erik On 4 Jul 2014, at 19:47, do...@iflysib.unlp.edu.ar wrote: Hi Erik Thanks. Details: System: proteins Properties: those ones for which there are analyzes tools in Gromacs I am trying to model some proteins at acid medium. I use MD with water and I create a physiological solution from the counterion tool of Gromacs, But I think something is wrong. To analize properties: I use RMSD of alfa carbons to test the converge of the MD. Also the idea is to analyze the giration radii and the fluctuations through the Raddi of Giration and the RMSDF tools that gives Gromacs. I realize now that Ia use the neutral protonate states for the proteins when I use the physiological solution, and this is an error. So, the results in RMSD, RG and RMSDF should be different from those that I have now. Sorry, I'm not a chemistry nor a biochemistry. I am a physics, so I have some missing concepts. Kind regards Chris I do not known if it is another different way to do the medium Erik Marklund erik.markl...@chem.ox.ac.uk ha escrito: Hi Chris, This very much depends on what system you are studying and what properties you aim to look at. Could you provide more detail please. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 4 Jul 2014, at 16:45, do...@iflysib.unlp.edu.ar wrote: Dear all Please, I need help. I have to do a simulation at an acid medium (PH = around 5 or 6). Is it sufficient to work with normal water,from it to create a physiological solution (Ph=around 5) and then to work with the physiological solution? I would very much appreciate any clues in this regards Chris Dra. M. Cristina Donnamaria Instituto de Fisica de Liqidos y Sistemas Biologicos -IFLYSIB- Comision de Invegtigaciones Cientificas de la Prov. de Bs. As. Argentina This message was sent using IMP, the Internet Messaging Program. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support
[gmx-users] Constant pH simulations
Hi everyone, I was wondering if anyone has any experience or knows of a tutorial site that I could look at for performing constant pH simulations. I've checked out the info on the gromacs.org web site and a few others such as (http://www.mpibpc.mpg.de/247796/usage) but I was wondering if there is anything more up to date than what I've found so far. Cheers, -Douglas Grahame BSc. MSc. PhD. Candidate dgrah...@uoguelph.ca --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Truncated .trr file size - 20% smaller than expected
Hi there this is my first time posting here so my apologies if I disregard any general formatting rules! In any event on to my question/problem. I am fairly new to MD simulations with much more background on the biological side than the simulation side. That being said, I have been receiving training from another member in the lab and have just started my simulations of a 325 residue protein using GROMACS 4.5.5. My issue has come from the fact that when I grompp my EM.mdp, NVT.mdp, or MPT.mdp files everything seems to be fine ie. No errors or issues and the file sizes match the expected output size. However, when I run my simulation I'm getting about a %20 decrease in the size of my .trr file from what it expects. From my .out file for the molecular dynamics run I get 'WARNING: This run will generate roughly 24940 Mb of data' Actual amount of data produced is ~18 Gb of data. There are no errors running gmx_check on any of the tpr files are anything else I've tried running the same simulation on two different supercomputing clusters to see if the same error occurs just in case it was an issue of the build version having any effect on the size and run into the same problems I've tried running the simulation in parts just in case there was some memory issue causing some problem that I wasn't aware of or looking for I've gotten my labmate and one more person familiar with GROMACS to look at my issued commands and they seem stumped I've also tried running it on 4.6.3 with the verlet cutoff scheme as I was having some issues with pp/pme load balance Nothing so far has made a difference and although the data seems to be fine I'm loathe to do all the analysis if there is something majorly wrong with my simulation. Problem for me is I don't know if or by how much the actual trr file size should change from the expected amounts. Command submitted: mdrun_mpi -npme -1 -s MD.tpr -o MD.trr -x MD.xtc -c MD.pdb -e MD.edr -g MD.log -v -dlb yes -cpo MD.cpt I am running/wanting to run my simulations for 25 - 50ns Thanks in advance for any help and all the best! -Doug --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
