Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/27/12 8:50 AM, J Peterson wrote: 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. With layered systems, the COM removal groups are best set to whatever makes physical sense - whatever is an integral part of a layer is a viable group. So I would think that any prosthetic group or ligand bound within a protein is a valid member of that layer. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999759.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/24/12 2:49 AM, J Peterson wrote: 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 lower)? In principle, no. It sounds like you have an asymmetric protein, which thus requires an asymmetric modification to the bilayer. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 lower)? Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999633.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 24/07/2012 2:57 PM, J Peterson wrote: 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 instead of adding them also inside the membrane, to reduce the system size ? Can we do magic here with any commands to add SOL molecules only single side of the membrane? Yes, but you'll need solvent on both sides else you're not modelling a solvated bilayer and will have to argue why your results are relevant. Further, if the z-direction is periodic then there is only one side to your bilayer anyway... If you really want to remove the solvent, and your bilayer is oriented parallel to the xy-plane, then there's several techniques that can filter solvent molecules based on their z-coordinate. Simplest is removing them by hand in a text editor, but g_select can make an index group that trjconv can remove. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 instead of adding them also inside the membrane, to reduce the system size ? Can we do magic here with any commands to add SOL molecules only single side of the membrane? Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999625.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/23/12 7:53 AM, J Peterson wrote: 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 was trying to do simulation only with this TM region and then attaching the rest of the protein with this TM region and simulate the whole system. But was time-taking. Can you please guide me to pack the lipid bilayer only around a 33-residues long peptide in my protein and rest with water? Position your protein manually using editconf -center such that it is placed appropriately relative to the membrane and follow the same procedure in the tutorial. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 was trying to do simulation only with this TM region and then attaching the rest of the protein with this TM region and simulate the whole system. But was time-taking. Can you please guide me to pack the lipid bilayer only around a 33-residues long peptide in my protein and rest with water? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999605.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/23/12 5:31 AM, J Peterson wrote: 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 bilayer) a long and thick bilayer to accommodate a large protein? Are there any experimental evidence about the thickness of the membrane that should be followed before expanding the membrane? You can expand a membrane patch in the x-y plane using genconf -nbox. That will give you a greater lateral size to work with. I don't know what exactly you mean by making the membrane thicker. Each lipid has an experimentally determined thickness (usually P-P distance) under given conditions (temperature, ionic strength, etc). In physiological membranes, proteins will tilt or kink due to hydrophobic mismatch if their dimensions exceed that of the hydrophobic core. If you need something that has a thicker hydrophobic core, then you may need to be looking into building your own membranes from scratch. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 bilayer) a long and thick bilayer to accommodate a large protein? Are there any experimental evidence about the thickness of the membrane that should be followed before expanding the membrane? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999602.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Error in Membrane simulations with POPC bilayer (
> 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 > > What do they really mean? Is the system safe with these notes? > > Peterson J Peterson J -- These are not errors, as you say in the title, but just notes, and I think they mean exactly what is written. What force field are you using for a POPC bilayer? Just curious... Cordially, Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/17/12 4:05 AM, J Peterson wrote: 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 http://manual.gromacs.org/online/mdp_opt.html#out nstcalcenergy tries to improve performance by reducing global communication. If you set nstcomm to a more frequent interval of steps, you're doing global communication more frequently, hence making nstcalcenergy relatively pointless, so grompp sets them both to nstcalcenergy for efficiency. NOTE 2 [file pr_NPT.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 As stated in the manual, NH chains > 1 can only be used with a velocity verlet integrator. What do they really mean? Is the system safe with these notes? Yes. These are normal messages. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 What do they really mean? Is the system safe with these notes? Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999483.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/13/12 6:44 AM, J Peterson wrote: 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 do it? Position the protein with editconf -center and follow all the other steps in the same way. The dimensions of the box become quite important in such a case. There are some general tips on such placement in another of my tutorials: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/03_tricks.html -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 do it? Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999409.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/13/12 4:14 AM, J Peterson wrote: 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? The strong restraints are only needed for InflateGRO. During equilibration, position restraints with a normal magnitude are appropriate. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/13/12 1:44 AM, J Peterson wrote: 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)? The box should be sufficiently large so as to avoid spurious interactions across periodic boundaries. The size is thus motivated by the length of the cutoffs used. Increasing the box by 1.0 nm might be just enough, but you should calculate this very carefully. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999401.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999395.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/13/12 12:24 AM, J Peterson wrote: 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? InflateGRO removes all solvent molecules. I also see one of the POPC molecules standing out (upside down) of the bilayer area. How would that be adjusted? http://gromacs.5086.n6.nabble.com/file/n4999393/POPC..jpg You need a bigger box. The lipids are moving into a neighboring periodic cell, which in itself is not a problem, but I suspect you'll have inadequate hydration and thus you'll be calculating headgroup-headgroup interactions across periodic boundaries, which you probably want to avoid. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 also see one of the POPC molecules standing out (upside down) of the bilayer area. How would that be adjusted? http://gromacs.5086.n6.nabble.com/file/n4999393/POPC..jpg Thanks Peterson -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999393.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/12/12 10:23 PM, J Peterson wrote: 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 confirm with you. During shrinking stage, I get the following notes, please tell me are they OK at this stage, NOTE 1 [file topol.top, line 3070]: System has non-zero total charge: 5.00e+00 Assuming this is the net charge on your protein, there's nothing wrong here. Analysing residue names: There are:46Protein residues There are: 126 Other residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 21063.00 Largest charge group radii for Van der Waals: 0.249, 0.247 nm Largest charge group radii for Coulomb: 0.249, 0.247 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 160x160x48, spacing 0.110 0.114 0.119 Estimate for the relative computational load of the PME mesh part: 0.92 NOTE 2 [file em_st.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing PME load for EM runs is usually irrelevant. During actual MD, you'd strive for better balance, but since an inflated lipid system in vacuo is rather weird, you can ignore this as well. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 confirm with you. During shrinking stage, I get the following notes, please tell me are they OK at this stage, NOTE 1 [file topol.top, line 3070]: System has non-zero total charge: 5.00e+00 Analysing residue names: There are:46Protein residues There are: 126 Other residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 21063.00 Largest charge group radii for Van der Waals: 0.249, 0.247 nm Largest charge group radii for Coulomb: 0.249, 0.247 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 160x160x48, spacing 0.110 0.114 0.119 Estimate for the relative computational load of the PME mesh part: 0.92 NOTE 2 [file em_st.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 17 Mb of data There were 2 notes Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999391.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/12/12 4:59 AM, J Peterson wrote: 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 topologies #include "gromos53a6_lipid.ff/ions.itp" ; System specifications [ system ] 128-Lipid POPC Bilayer [ molecules ] ; molecule name nr. POPC 128 SOL 2460 And the following is the first part of my popc128b.gro file Alm on surf + relaxed popc 14036 1POP C11 0.253 5.425 1.688 1POP C22 0.428 5.314 1.792 1POP C33 0.334 5.243 1.571 1POP N44 0.378 5.352 1.660 1POP C55 0.474 5.439 1.590 1POP C66 0.606 5.390 1.531 1POP O77 0.692 5.366 1.643 1POP P88 0.834 5.316 1.587 1POP O99 0.800 5.197 1.505 1POPO10 10 0.903 5.435 1.533 1POPO11 11 0.890 5.266 1.729 1POPC12 12 0.823 5.142 1.753 1POPC13 13 0.836 5.086 1.895 1POPO14 14 0.766 4.964 1.924 1POPC15 15 0.632 4.959 1.944 1POPO16 16 0.555 5.019 1.869 1POPC17 17 0.589 4.833 2.020 1POPC18 18 0.615 4.703 1.944 1POPC19 19 0.595 4.575 2.025 1POPC20 20 0.625 4.467 1.920 1POPC21 21 0.677 4.340 1.987 1POPC22 22 0.813 4.357 2.055 1POPC23 23 0.848 4.223 2.120 1POPC24 24 0.884 4.121 2.012 1POPC25 25 0.957 4.013 2.043 1POPC26 26 0.994 3.986 2.189 1POPC27 27 1.069 3.853 2.202 1POPC28 28 0.967 3.739 2.204 1POPC29 29 1.012 3.593 2.202 1POPC30 30 0.916 3.478 2.169 1POPC31 31 0.869 3.518 2.029 1POPC32 32 0.801 5.205 1.983 . . . . . What are the parts mismatching in these files? From what's shown, it's impossible to tell. Based on this information, everything lines up. I'm assuming the original coordinate file and the popc.itp topology came from Tieleman's site? Since it says the atom names from the top file will be used, is it safe to ignore this warning too? No. The naming mismatches imply that grompp is trying to map parameters for lipids onto water molecules. The resulting simulation will be nonsense and will probably crash immediately. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[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 topologies #include "gromos53a6_lipid.ff/ions.itp" ; System specifications [ system ] 128-Lipid POPC Bilayer [ molecules ] ; molecule name nr. POPC 128 SOL 2460 And the following is the first part of my popc128b.gro file Alm on surf + relaxed popc 14036 1POP C11 0.253 5.425 1.688 1POP C22 0.428 5.314 1.792 1POP C33 0.334 5.243 1.571 1POP N44 0.378 5.352 1.660 1POP C55 0.474 5.439 1.590 1POP C66 0.606 5.390 1.531 1POP O77 0.692 5.366 1.643 1POP P88 0.834 5.316 1.587 1POP O99 0.800 5.197 1.505 1POPO10 10 0.903 5.435 1.533 1POPO11 11 0.890 5.266 1.729 1POPC12 12 0.823 5.142 1.753 1POPC13 13 0.836 5.086 1.895 1POPO14 14 0.766 4.964 1.924 1POPC15 15 0.632 4.959 1.944 1POPO16 16 0.555 5.019 1.869 1POPC17 17 0.589 4.833 2.020 1POPC18 18 0.615 4.703 1.944 1POPC19 19 0.595 4.575 2.025 1POPC20 20 0.625 4.467 1.920 1POPC21 21 0.677 4.340 1.987 1POPC22 22 0.813 4.357 2.055 1POPC23 23 0.848 4.223 2.120 1POPC24 24 0.884 4.121 2.012 1POPC25 25 0.957 4.013 2.043 1POPC26 26 0.994 3.986 2.189 1POPC27 27 1.069 3.853 2.202 1POPC28 28 0.967 3.739 2.204 1POPC29 29 1.012 3.593 2.202 1POPC30 30 0.916 3.478 2.169 1POPC31 31 0.869 3.518 2.029 1POPC32 32 0.801 5.205 1.983 . . . . . What are the parts mismatching in these files? Since it says the atom names from the top file will be used, is it safe to ignore this warning too? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999354.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
