[gmx-users] RE: RE: RE: Doubts over g_lie usage

Thank you so much for your time and explanation. I am recalculating the energy co-ordinates and using it in g_lie calculations. I have read the manual and changed the .mdp file I am using. The following is the mdp file, please check for the correctness. The text in bold font are newly included

[gmx-users] RE: RE: Doubts over g_lie usage

Thanks for that explanation. I would like to know this with little more detail. What do you mean by RF-0 and which cut-off value are you talking about? Rerunning the trajectory means the whole MD run again? Thanks. -- View this message in context:

[gmx-users] Doubts over g_lie usage

Hello everyone, I have a doubt about LIE calculation using g_lie in gromacs. This doubt is about the values automatically assigned for -Clj and -Cqq flags when I ran the following command: $ g_lie -f J32_md10ns.edr -o LIE_1A1_J32.xvg -b 7001 -e 1 -ligand J32 The following text contains my

[gmx-users] RE: Doubts over g_lie usage

Dear Tom, The explanation really helps me understand LIE much more clearer. What's the issue if I have used PME coulombtype? I have actually used PME. Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Doubts-over-g-lie-usage-tp5000130p5000146.html Sent

[gmx-users] RE: tutorials for Coarse-Grained MD Simulation

Thank you so much for clearing my doubt. I have another doubt that how can I use g_fg2cg program in reverse transformation (RT) while this program is not an internal GROMACS program. The RT tutorial in MARTINI website says that one has to compile and source the files from rev_trans.tar.gz. How

[gmx-users] RE: tutorials for Coarse-Grained MD Simulation

Dear Jan, Thanks for the link. The tutorials available here are very helpful start preparing the systems for simulation but would like to know how to merge the custom version of Gromacs for CG available in Martini web site with my existing Gromacs installation. Moreover how to make use of all

[gmx-users] tutorials for Coarse-Grained MD Simulation

Dear Gromacs Users, I would like to know if there are any tutorials for Coarse-Grained MD Simulation available anywhere. Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/tutorials-for-Coarse-Grained-MD-Simulation-tp467.html Sent from the GROMACS Users

[gmx-users] LIE using g_lie

Dear colleagues, I have some doubts about LIE and would like some clarifications. While I calculate the LIE using g_lie, it gives the DGbind energy in KJ/mol and a standard deviation in parentheses. How well can I use this value alone or meaningful it is by itself in comparing the binding

[gmx-users] Re: Linear Interaction energy calculations

Dear colleagues, Thanks for opening up this topic. I also have some doubts about LIE and would like some clarifications. While I calculate the LIE using g_lie, it gives the DGbind energy in KJ/mol and a standard deviation in parentheses. How well can we use this value alone or meaningful it is

[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Hi Justin, Thanks for that information. I also would like to confirm with you that should I combine my metal ion too while I combine Protein and POPC into Protein_POPC group to be used in COMM removal? So that I will have a group Protein_HEM_POPC. Thanks Peterson J -- View this message in

[gmx-users] Re: question about minimisation

Hi, Did you call your genrestr output in your mdp file using define = * ? (for example define = -DPOSRES ; where posres was your file name.) Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/question-about-minimisation-tp4999681p4999685.html Sent from the

[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Thanks for that comment. I've another query during inflating step in Justin's tutorial. In my case, during the inflation, 4 lipids from the upper and 2 lipids from the lower leaflets were removed. Would there be a problem in this sort non-uniform deletion (I mean like 4 from upper and 4 from

[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Hi Justin, Thanks for all your help to get me through membrane simulations. I've a problem to be solved. I need a long and thick membrane to simulate a big protein. The longest bilayer that I can download from Tieleman's website is 64 molecules long. How can I make (double or triple the

[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Thank you so much for that, Justin. Now I could expand the bilayer. I've another query. My protein has a small N-terminal portion embedded in the membrane, I would like to insert only this part into the membrane during 'packing the lipid around the protein' step in your tutorial. Initially I

[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Hi Justin, That works really fine and thanks. Now, how can I add additional SOL molecules only one side of the bilayer (either upper or lower)? Since my protein binds at the outer side (extracellular region) of the membrane I can only fill the upper (extracellular) region with SOL molecules

[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Hi Justin, I have the following Notes during NPT equilibration. NOTE 1 [file pr_NPT.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file pr_NPT.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Hi Justin, I have another doubt on the strong posres that was included in the topology file. When do we need to remove that position restraint? Does it really affect at point of time the system? Thanks Peterson J -- View this message in context:

[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Thanks Justin, The explanations are very very useful during my course of simulating a protein with POPC. I also would like to get explanation on how to simulate a protein which has only its N-terminal region embedded in the membrane but the rest in solvent. What is the easy and accurate way to

[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Hi Justin, Thanks for the effort to help me. I still no out of the error. The following is the content of my topol_popc.top ; Include chain topologies #include gromos53a6_lipid.ff/forcefield.itp #include popc.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp ; Include ion

[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Hi Justin, Thanks for the suggestion I got it solved somehow. The main problem was in the popc128b.pdb itself, it has first 64 lipids and half of the SOl molecules followed by rest of the POPC and SOL molecules. When I rearranged them the error was solved. But now another thing I would like to

[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Hi Justin, I followed your comments and now at the stage of adding solvents. I wonder to see the protein after shrinking step to have no SOL molecules as there were SOL molecules in the source popc128b.pdb. Had we removed all the original SOL molecules anywhere during the course of tutorial? I

[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Thanks for the comment. By the way how to make a bigger box at this time of the tutorial without affecting any part of the system. Can I use editconf with slightly bigger number for z-axis (something like 6.7 which was 5.7 before)? Thanks Peterson J -- View this message in context:

[gmx-users] Error in Membrane simulations with POPC bilayer

Hi Justin and Anirban, I started a membrane simulation with POPC bilayer after a training with the given KALP peptide and DPPC bilayer. I am following both of your tutorials (mainly the Justin's). I have problem at where I generate a .tpr file for a DPPC (POPC here)-only system using grompp. I

[gmx-users] MD simulation with varying pH

Dear GROMACS Users, I'm planning to work on a protein that activates itself under lower pH conditions. And I don't have any clues how to do it in GROMACS. My first question is about the possibilities to do this in GROMACS, has anyone done this before? It can even be a constant simulations at a

[gmx-users] AMBER heme parameters to simulate in GROMACS

Dear colleagues, Has anyone run simulation with heme moiety in GROMACS with AMBER FF before? I have a problem running it. I need the topology parameters for the heme. Thanks Peterson -- View this message in context:

[gmx-users] Re: Fwd: HEME-cysteine gromacs simulation

Zhang Bing, I guess it is problem in your visualizers. Try to label the atom using VMD which goes well with most of the file types derived in GROMACS. I hope you'll see the atom as FE not just F. Thanks Peterson -- View this message in context: