Re: [gmx-users] Coordinate file for lipid bilayer
To generate starting (non-equilibrated) bilayer structures for use in MD simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/. Otherwise, for conventional lipids CHARMM-GUI membrane builder (http://www.charmm-gui.org/?doc=input/membrane). Hope it helps! Felipe On 10/04/2012 07:46 AM, James Starlight wrote: Justin, lastly, is there any other ways to obtain bilayers of desired dimensions started from just one lipid oriented in desired way for instance? James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 12:38 PM, James Starlight wrote: Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). My advice is still the same - you need box vectors that are compatible with both a sensible water layer and membrane leaflets. -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 * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Coordinate file for lipid bilayer
Dear Felipe, thanks for advise. Does the Packmol software suitable for generation coordinates of the bergers ( for gromos 56 ff) lipids ? As I know CHARMM-GUI membrane builder is suitable for only CHARMM force field lipids. James 2012/10/4 Felipe Pineda, PhD luis.pinedadecas...@lnu.se: To generate starting (non-equilibrated) bilayer structures for use in MD simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/. Otherwise, for conventional lipids CHARMM-GUI membrane builder (http://www.charmm-gui.org/?doc=input/membrane). Hope it helps! Felipe On 10/04/2012 07:46 AM, James Starlight wrote: Justin, lastly, is there any other ways to obtain bilayers of desired dimensions started from just one lipid oriented in desired way for instance? James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 12:38 PM, James Starlight wrote: Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). My advice is still the same - you need box vectors that are compatible with both a sensible water layer and membrane leaflets. -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 * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Coordinate file for lipid bilayer
Hi, packmol generates just coordinates (pdb format) for optimized packing arrangements of whatever molecule you provide as input. It's up to you to parameterize the resulting model. CHARMM-GUI has a library of conventional (phospho)lipids and generates the input for CHARMM equilibration of the bilayer model built with those lipids. But, you should inspect by yourself the corresponding sites. Felipe On 10/04/2012 03:11 PM, James Starlight wrote: Dear Felipe, thanks for advise. Does the Packmol software suitable for generation coordinates of the bergers ( for gromos 56 ff) lipids ? As I know CHARMM-GUI membrane builder is suitable for only CHARMM force field lipids. James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Coordinate file for lipid bilayer
Hi James, The bilayers from the CHARMM-GUI can be converted into any force field using a simple script. For a united-atom force field you will need to remove the non-polar hydrogens, rename the atoms and possibly reorder some of the atoms in the lipids. As for other methods to build membranes, there are numerous different methods available. One of the simplest approaches is to use genconf to replicate a single lipid up to the desired size of membrane and perform and simulation to equilibrate the properties of your membrane (although depending upon the lipid and force field this may require simulations in the order of several hundreds of ns though). Another fairly simple method (which can also be easily used to make hexagonal membranes) is to self-assemble a coarse-grained membrane, map that back to an atomistic representation (using one of a number of available tools) and equilibrate. One issue using this method is that the self-assembly often results in uneven numbers of lipids per membrane leaflet. This, however, is easy to correct after the self-assembly. Cheers Tom James Starlight wrote: Dear Felipe, thanks for advise. Does the Packmol software suitable for generation coordinates of the bergers ( for gromos 56 ff) lipids ? As I know CHARMM-GUI membrane builder is suitable for only CHARMM force field lipids. James 2012/10/4 Felipe Pineda, PhD luis.pinedadecas...@lnu.se: To generate starting (non-equilibrated) bilayer structures for use in MD simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/. Otherwise, for conventional lipids CHARMM-GUI membrane builder (http://www.charmm-gui.org/?doc=input/membrane). Hope it helps! Felipe On 10/04/2012 07:46 AM, James Starlight wrote: Justin, lastly, is there any other ways to obtain bilayers of desired dimensions started from just one lipid oriented in desired way for instance? James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 12:38 PM, James Starlight wrote: Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). My advice is still the same - you need box vectors that are compatible with both a sensible water layer and membrane leaflets. -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 * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Coordinate file for lipid bilayer
On 10/3/12 1:59 AM, James Starlight wrote: Justin, I've told about lower lipid density at the left and right edges of the new system ( see new pic bellow with marked regions). http://imageshack.us/photo/my-images/10/dppc.png/ I've started with system consisted of 118 lipids and 6000 water in dims 6x6x10 I've created new box with the desired sizes for my system as well as centered it in it. Finally I've resized it via genbox -cp prot_in_lipids_old.gro -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156 As the result I've obtain syste of 128 lipids and 13000 water with dims 8x8x10 I have the same system with the popc lipids with the same dims where there are 200 lipids Why only 10 lipids were added after resizing ? How I could increase this number of added lipids ( expesially in regions with lower lipid density- see pic) ? genbox decides whether or not to put molecules in the box if they can be added intact; anything sticking out of the box is removed. Since water molecules are small, this is easy to do. Since a lipid molecule is large, it is not so easy. The hydrocarbon tails are very flexible and thus may have configurations leading them to stick out of the box, so genbox won't add them. You will likely have to gradually increase the box dimensions in x and y to allow for more lipids to be added, striking a balance between the (much larger) number of water molecules and number of lipids added. -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 * 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] Coordinate file for lipid bilayer
Justin, Might the modifications of the vdwradii.dat be suitable for such system expanding or (on other hand) reduction (as in the below picture are shown). In the lattter case I defined new box dimensions (smaller than initial box dims) and would like to remove all side water-lipids layer which are beyond new pbc dimensions)? http://imageshack.us/content_round.php?page=donel=img138/5497/reduction.png James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 1:59 AM, James Starlight wrote: Justin, I've told about lower lipid density at the left and right edges of the new system ( see new pic bellow with marked regions). http://imageshack.us/photo/my-images/10/dppc.png/ I've started with system consisted of 118 lipids and 6000 water in dims 6x6x10 I've created new box with the desired sizes for my system as well as centered it in it. Finally I've resized it via genbox -cp prot_in_lipids_old.gro -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156 As the result I've obtain syste of 128 lipids and 13000 water with dims 8x8x10 I have the same system with the popc lipids with the same dims where there are 200 lipids Why only 10 lipids were added after resizing ? How I could increase this number of added lipids ( expesially in regions with lower lipid density- see pic) ? genbox decides whether or not to put molecules in the box if they can be added intact; anything sticking out of the box is removed. Since water molecules are small, this is easy to do. Since a lipid molecule is large, it is not so easy. The hydrocarbon tails are very flexible and thus may have configurations leading them to stick out of the box, so genbox won't add them. You will likely have to gradually increase the box dimensions in x and y to allow for more lipids to be added, striking a balance between the (much larger) number of water molecules and number of lipids added. -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 * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Coordinate file for lipid bilayer
On 10/3/12 8:59 AM, James Starlight wrote: Justin, Might the modifications of the vdwradii.dat be suitable for such system expanding or (on other hand) reduction (as in the below picture are shown). In the lattter case I defined new box dimensions (smaller than initial box dims) and would like to remove all side water-lipids layer which are beyond new pbc dimensions)? http://imageshack.us/content_round.php?page=donel=img138/5497/reduction.png I don't know if that will have much of an effect or not. The values in vdwradii.dat are used to determine if there is atomic overlap with coordinates being added (solvent) to the solute configuration. -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 * 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] Coordinate file for lipid bilayer
Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 8:59 AM, James Starlight wrote: Justin, Might the modifications of the vdwradii.dat be suitable for such system expanding or (on other hand) reduction (as in the below picture are shown). In the lattter case I defined new box dimensions (smaller than initial box dims) and would like to remove all side water-lipids layer which are beyond new pbc dimensions)? http://imageshack.us/content_round.php?page=donel=img138/5497/reduction.png I don't know if that will have much of an effect or not. The values in vdwradii.dat are used to determine if there is atomic overlap with coordinates being added (solvent) to the solute configuration. -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 * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Coordinate file for lipid bilayer
On 10/3/12 12:38 PM, James Starlight wrote: Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). My advice is still the same - you need box vectors that are compatible with both a sensible water layer and membrane leaflets. -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 * 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] Coordinate file for lipid bilayer
Justin, lastly, is there any other ways to obtain bilayers of desired dimensions started from just one lipid oriented in desired way for instance? James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 12:38 PM, James Starlight wrote: Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). My advice is still the same - you need box vectors that are compatible with both a sensible water layer and membrane leaflets. -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 * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Coordinate file for lipid bilayer
Dear all! Recently I've forced with the same problem as was in this topic :) I have tieleman's lipids consisted of 128 dppc with water. also I have system with the protein inserted in the same bilayer I wounder to know 1- How I could change lipid number in the pure lipid bilayer ( increase up to 200 lipids) with standard Gromacs tools ? I've tried use genbox -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156 where 8.045 in x and y was higher than in the case of initial bilayer ( 6.045) As the consequence that prodyce larger system with increased amount of water in upper and lower layers but the lipid number was the same. 2- Is there any way to increase lipid number ( to add lipids from each size of the system) in the bilayer with the inserted protein ? Thanks for help, James 2012/6/11, Justin A. Lemkul jalem...@vt.edu: On 6/11/12 6:05 AM, James Starlight wrote: Dear all! Recently I've forced with the opposite problem. I have pre-equilbrated bilayer of highter dimensions than I need. How I could reduce lipid number of such bilayer as well as reduce total dimensions of such system ? E.g I have preequilibrated bilayer consisted of 340 lipids. I want to reduce it to the 200 lipids by the symmetrical deletion of the unnecessary lipids from each side. Is there simplest way to do it ? Try genbox with the -box option (with your bilayer as -cs) to set a smaller box size that will give a suitable number of lipids. -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 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Coordinate file for lipid bilayer
On 10/2/12 2:16 PM, James Starlight wrote: Dear all! Recently I've forced with the same problem as was in this topic :) I have tieleman's lipids consisted of 128 dppc with water. also I have system with the protein inserted in the same bilayer I wounder to know 1- How I could change lipid number in the pure lipid bilayer ( increase up to 200 lipids) with standard Gromacs tools ? I've tried use genbox -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156 where 8.045 in x and y was higher than in the case of initial bilayer ( 6.045) As the consequence that prodyce larger system with increased amount of water in upper and lower layers but the lipid number was the same. The proper approach is to set values for the box that are larger in x and y, but the same size in z. That way, the new solvation occurs within the same plane as the membrane. 2- Is there any way to increase lipid number ( to add lipids from each size of the system) in the bilayer with the inserted protein ? Using the same approach, with a slight modification: genbox -cp protein_in_membrane.gro -cs dppc128_whole.gro -box (x y z) Increase the values of x and y, and leave z alone. -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 * 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] Coordinate file for lipid bilayer
Justin, I've done exactly like you provide me ( changing only x and y ) but in that case the protein and the old lipids were slightly shifted to one side of the new system. Is there any way to center the old system in respect to the new solvent ? Also I've noticed that when I increase size of my system in x and y dimensions both of the water layers were increased greatly than lipid layer ( it's look like sandwich with two big bread pieces and smaller cutlet between them :) ) James 2012/10/2, Justin Lemkul jalem...@vt.edu: On 10/2/12 2:16 PM, James Starlight wrote: Dear all! Recently I've forced with the same problem as was in this topic :) I have tieleman's lipids consisted of 128 dppc with water. also I have system with the protein inserted in the same bilayer I wounder to know 1- How I could change lipid number in the pure lipid bilayer ( increase up to 200 lipids) with standard Gromacs tools ? I've tried use genbox -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156 where 8.045 in x and y was higher than in the case of initial bilayer ( 6.045) As the consequence that prodyce larger system with increased amount of water in upper and lower layers but the lipid number was the same. The proper approach is to set values for the box that are larger in x and y, but the same size in z. That way, the new solvation occurs within the same plane as the membrane. 2- Is there any way to increase lipid number ( to add lipids from each size of the system) in the bilayer with the inserted protein ? Using the same approach, with a slight modification: genbox -cp protein_in_membrane.gro -cs dppc128_whole.gro -box (x y z) Increase the values of x and y, and leave z alone. -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 * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Coordinate file for lipid bilayer
On 10/2/12 2:56 PM, James Starlight wrote: Justin, I've done exactly like you provide me ( changing only x and y ) but in that case the protein and the old lipids were slightly shifted to one side of the new system. Is there any way to center the old system in respect to the new solvent ? Define a new box and center with editconf -c -box. Also I've noticed that when I increase size of my system in x and y dimensions both of the water layers were increased greatly than lipid layer ( it's look like sandwich with two big bread pieces and smaller cutlet between them :) ) This suggests that something is wrong with the z-dimension. I only say that because you had a 10-nm z-length in your previous post with the Tieleman DPPC bilayer, which is far larger than the coordinate file normally has. genbox works by tiling the solvent coordinates through the empty space in the solute configuration. If you're expanding in 3 dimensions, you can expect weird things to happen with membrane systems. -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 * 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] Coordinate file for lipid bilayer
Justin Previously I've expanded initial system on Z-dim before the protein was inserted to increase both water layers. After current processing with Genbox there is no problems in Z actually- it look likes sandwich with two broader bread layers and narrower cutlet :) So the lipid layer in x and y is thinker than water ( so the lipid number stay the same after resizing). James 2012/10/2, Justin Lemkul jalem...@vt.edu: On 10/2/12 2:56 PM, James Starlight wrote: Justin, I've done exactly like you provide me ( changing only x and y ) but in that case the protein and the old lipids were slightly shifted to one side of the new system. Is there any way to center the old system in respect to the new solvent ? Define a new box and center with editconf -c -box. Also I've noticed that when I increase size of my system in x and y dimensions both of the water layers were increased greatly than lipid layer ( it's look like sandwich with two big bread pieces and smaller cutlet between them :) ) This suggests that something is wrong with the z-dimension. I only say that because you had a 10-nm z-length in your previous post with the Tieleman DPPC bilayer, which is far larger than the coordinate file normally has. genbox works by tiling the solvent coordinates through the empty space in the solute configuration. If you're expanding in 3 dimensions, you can expect weird things to happen with membrane systems. -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 * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Coordinate file for lipid bilayer
On 10/2/12 3:49 PM, James Starlight wrote: Justin Previously I've expanded initial system on Z-dim before the protein was inserted to increase both water layers. After current processing with Genbox there is no problems in Z actually- it look likes sandwich with two broader bread layers and narrower cutlet :) So the lipid layer in x and y is thinker than water ( so the lipid number stay the same after resizing). Posting a link to an actual image would be really useful here. I'm not sure I understand your metaphor exactly. If you're looking to add lipids and water around an existing system, the z-dimension of the solute and solvent boxes have to be the same. So if you have a system that you have extended in z to accommodate a protein or whatever else, you need to manipulate a DPPC-only system in the same way - extend its z-dimension to be the same as the solute, maintaining the relative position of the membrane within the new solvent box, and then add water in the solvent configuration to fill that box. Then proceed as I've suggested before. It should be obvious from all of this that it is vastly easier to plan a box of sufficient size before starting ;) -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 * 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] Coordinate file for lipid bilayer
This is exactly what I've obtained http://imageshack.us/photo/my-images/27/89293914.png/ the same effect was also in case of intact tieleman's lipid bilayers ( the water layers were broader than lipid after resizing with genbox) James 2012/10/2, Justin Lemkul jalem...@vt.edu: On 10/2/12 3:49 PM, James Starlight wrote: Justin Previously I've expanded initial system on Z-dim before the protein was inserted to increase both water layers. After current processing with Genbox there is no problems in Z actually- it look likes sandwich with two broader bread layers and narrower cutlet :) So the lipid layer in x and y is thinker than water ( so the lipid number stay the same after resizing). Posting a link to an actual image would be really useful here. I'm not sure I understand your metaphor exactly. If you're looking to add lipids and water around an existing system, the z-dimension of the solute and solvent boxes have to be the same. So if you have a system that you have extended in z to accommodate a protein or whatever else, you need to manipulate a DPPC-only system in the same way - extend its z-dimension to be the same as the solute, maintaining the relative position of the membrane within the new solvent box, and then add water in the solvent configuration to fill that box. Then proceed as I've suggested before. It should be obvious from all of this that it is vastly easier to plan a box of sufficient size before starting ;) -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 * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Coordinate file for lipid bilayer
On 10/2/12 4:12 PM, James Starlight wrote: This is exactly what I've obtained http://imageshack.us/photo/my-images/27/89293914.png/ This looks completely normal. What I was asking for was an image of one of your failed attempts that has whatever odd manifestation you've been trying to describe. the same effect was also in case of intact tieleman's lipid bilayers ( the water layers were broader than lipid after resizing with genbox) Sorry, I still don't understand. I've explained as clearly as I can how to proceed, if you need further help you will have to provide the exact commands you're using and why they're insufficient (again, pictures of failed systems, not normal ones, would help here). -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 * 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] Coordinate file for lipid bilayer
Justin, I've told about lower lipid density at the left and right edges of the new system ( see new pic bellow with marked regions). http://imageshack.us/photo/my-images/10/dppc.png/ I've started with system consisted of 118 lipids and 6000 water in dims 6x6x10 I've created new box with the desired sizes for my system as well as centered it in it. Finally I've resized it via genbox -cp prot_in_lipids_old.gro -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156 As the result I've obtain syste of 128 lipids and 13000 water with dims 8x8x10 I have the same system with the popc lipids with the same dims where there are 200 lipids Why only 10 lipids were added after resizing ? How I could increase this number of added lipids ( expesially in regions with lower lipid density- see pic) ? James 2012/10/2, Justin Lemkul jalem...@vt.edu: On 10/2/12 4:12 PM, James Starlight wrote: This is exactly what I've obtained http://imageshack.us/photo/my-images/27/89293914.png/ This looks completely normal. What I was asking for was an image of one of your failed attempts that has whatever odd manifestation you've been trying to describe. the same effect was also in case of intact tieleman's lipid bilayers ( the water layers were broader than lipid after resizing with genbox) Sorry, I still don't understand. I've explained as clearly as I can how to proceed, if you need further help you will have to provide the exact commands you're using and why they're insufficient (again, pictures of failed systems, not normal ones, would help here). -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 * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Coordinate file for lipid bilayer
Dear all! Recently I've forced with the opposite problem. I have pre-equilbrated bilayer of highter dimensions than I need. How I could reduce lipid number of such bilayer as well as reduce total dimensions of such system ? E.g I have preequilibrated bilayer consisted of 340 lipids. I want to reduce it to the 200 lipids by the symmetrical deletion of the unnecessary lipids from each side. Is there simplest way to do it ? James 2012/5/28 Jon Kapla jon.ka...@mmk.su.se Hi, The easiest solution is probably to write a script that reorders the structure file (gro for example, just swap the lines in each lipid, and use editconf -f file.gro -resnr 1 to renumber) the way it is written in the topology. Cheers Jon On 2012-05-28 08:03, James Starlight wrote: Peter, Thanks for advise. I've found already pre-equilibrated POPC bilayers with 200 lipids. I've examined that lipids and found that they are very similar to the berger's lipids (it consists of equal nymber of atoms ) but the atom order in each lipid is slightly different than in Tieleman's popc.itp file so during processing of that lipids I've got error of non-matching atoms. Is there any trivial way to make new popc.itp based on existing gro file with correct atom order ? James 2012/5/26 Peter C. Lai p...@uab.edu Either use genbox -cs popc128b.gro or genconf -f popc128b.gro -nbox x y 0 Tieleman's lipids require you to generate a dummy tpr for use with trjconv to unwrap the pbc (trjconv -s em.tpr -f popc128b.pdb -o popc128b-nopbc.gro -pbc mol -ur compact) first. Lots of people have their own bilayer but they may be for different FFs which means the atom naming would not be immediately be compatible with your FF; for example mine are built for charmm36 and would require atom renaming for another FF, even charmm27. On 2012-05-26 11:24:12AM +0400, James Starlight wrote: Dear Gromacs Users! I want to perform MD simulation of my membrane protein in POPC or POPE bilayer using Tieleman's parameters for lipids by means of gromos united atom force field. The main problem is that the pre-equilibrated bilayers wich I found on the Dr. Tieleman's site consist of no more that 128 lipids but I want to simulate my protein with bigger number of lipids ( for example starting from 200 lipids ). What should I do in that case ? Could you provide me with some tools for construction of such united-atoms bilayers with desired dimensions ? Finally is there any others pre-equilibrated bilayers aviable for downloading besides Dr. Tieleman's site ? thanks for your help, James S. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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 -- _ Jon Kapla Division of Physical Chemistry Dpt. of Materials and Environmental Chemistry (MMK) Arrhenius Laboratory Stockholm University SE-106 91 Stockholm Pos:PhD Student Phone: +46 8 16 11 79 (office) Phone: +46 70 304 19 89 (cell) E-mail: jon.ka...@mmk.su.se _ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] Coordinate file for lipid bilayer
On 6/11/12 6:05 AM, James Starlight wrote: Dear all! Recently I've forced with the opposite problem. I have pre-equilbrated bilayer of highter dimensions than I need. How I could reduce lipid number of such bilayer as well as reduce total dimensions of such system ? E.g I have preequilibrated bilayer consisted of 340 lipids. I want to reduce it to the 200 lipids by the symmetrical deletion of the unnecessary lipids from each side. Is there simplest way to do it ? Try genbox with the -box option (with your bilayer as -cs) to set a smaller box size that will give a suitable number of lipids. -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 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] Coordinate file for lipid bilayer
Peter, Thanks for advise. I've found already pre-equilibrated POPC bilayers with 200 lipids. I've examined that lipids and found that they are very similar to the berger's lipids (it consists of equal nymber of atoms ) but the atom order in each lipid is slightly different than in Tieleman's popc.itp file so during processing of that lipids I've got error of non-matching atoms. Is there any trivial way to make new popc.itp based on existing gro file with correct atom order ? James 2012/5/26 Peter C. Lai p...@uab.edu Either use genbox -cs popc128b.gro or genconf -f popc128b.gro -nbox x y 0 Tieleman's lipids require you to generate a dummy tpr for use with trjconv to unwrap the pbc (trjconv -s em.tpr -f popc128b.pdb -o popc128b-nopbc.gro -pbc mol -ur compact) first. Lots of people have their own bilayer but they may be for different FFs which means the atom naming would not be immediately be compatible with your FF; for example mine are built for charmm36 and would require atom renaming for another FF, even charmm27. On 2012-05-26 11:24:12AM +0400, James Starlight wrote: Dear Gromacs Users! I want to perform MD simulation of my membrane protein in POPC or POPE bilayer using Tieleman's parameters for lipids by means of gromos united atom force field. The main problem is that the pre-equilibrated bilayers wich I found on the Dr. Tieleman's site consist of no more that 128 lipids but I want to simulate my protein with bigger number of lipids ( for example starting from 200 lipids ). What should I do in that case ? Could you provide me with some tools for construction of such united-atoms bilayers with desired dimensions ? Finally is there any others pre-equilibrated bilayers aviable for downloading besides Dr. Tieleman's site ? thanks for your help, James S. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] Coordinate file for lipid bilayer
Hi, The easiest solution is probably to write a script that reorders the structure file (gro for example, just swap the lines in each lipid, and use editconf -f file.gro -resnr 1 to renumber) the way it is written in the topology. Cheers Jon On 2012-05-28 08:03, James Starlight wrote: Peter, Thanks for advise. I've found already pre-equilibrated POPC bilayers with 200 lipids. I've examined that lipids and found that they are very similar to the berger's lipids (it consists of equal nymber of atoms ) but the atom order in each lipid is slightly different than in Tieleman's popc.itp file so during processing of that lipids I've got error of non-matching atoms. Is there any trivial way to make new popc.itp based on existing gro file with correct atom order ? James 2012/5/26 Peter C. Lai p...@uab.edu mailto:p...@uab.edu Either use genbox -cs popc128b.gro or genconf -f popc128b.gro -nbox x y 0 Tieleman's lipids require you to generate a dummy tpr for use with trjconv to unwrap the pbc (trjconv -s em.tpr -f popc128b.pdb -o popc128b-nopbc.gro -pbc mol -ur compact) first. Lots of people have their own bilayer but they may be for different FFs which means the atom naming would not be immediately be compatible with your FF; for example mine are built for charmm36 and would require atom renaming for another FF, even charmm27. On 2012-05-26 11:24:12AM +0400, James Starlight wrote: Dear Gromacs Users! I want to perform MD simulation of my membrane protein in POPC or POPE bilayer using Tieleman's parameters for lipids by means of gromos united atom force field. The main problem is that the pre-equilibrated bilayers wich I found on the Dr. Tieleman's site consist of no more that 128 lipids but I want to simulate my protein with bigger number of lipids ( for example starting from 200 lipids ). What should I do in that case ? Could you provide me with some tools for construction of such united-atoms bilayers with desired dimensions ? Finally is there any others pre-equilibrated bilayers aviable for downloading besides Dr. Tieleman's site ? thanks for your help, James S. -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu mailto:p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- _ Jon Kapla Division of Physical Chemistry Dpt. of Materials and Environmental Chemistry (MMK) Arrhenius Laboratory Stockholm University SE-106 91 Stockholm Pos:PhD Student Phone: +46 8 16 11 79 (office) Phone: +46 70 304 19 89 (cell) E-mail: jon.ka...@mmk.su.se _ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] Coordinate file for lipid bilayer
Sounds dangerous to me. Here's a possible methods section from your paper: we obtained a popc bilayer somewhere on the internet. Unfortunately, this structure did not match our topology file. Nevertheless, it has the same number of atoms and so we assumed that the difference was simply a matter of reordering ... (not too appealing I think). Peter's advice was good and I recommend avoiding a reordering based on an assumption that it will be correct. Using the method that Peter outlined, there will be some issues with equilibration at the new periodic boundary, but 100 ns of MD simulation should take care of that just fine (note that the Tieleman 128 lipid file is pretty old and, computers being slower then, I imagine that it was equilibrated with fewer than 100 ns itself). Chris. On 2012-05-28 08:03, James Starlight wrote: Peter, Thanks for advise. I've found already pre-equilibrated POPC bilayers with 200 lipids. I've examined that lipids and found that they are very similar to the berger's lipids (it consists of equal nymber of atoms ) but the atom order in each lipid is slightly different than in Tieleman's popc.itp file so during processing of that lipids I've got error of non-matching atoms. Is there any trivial way to make new popc.itp based on existing gro file with correct atom order ? James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] Coordinate file for lipid bilayer
Either use genbox -cs popc128b.gro or genconf -f popc128b.gro -nbox x y 0 Tieleman's lipids require you to generate a dummy tpr for use with trjconv to unwrap the pbc (trjconv -s em.tpr -f popc128b.pdb -o popc128b-nopbc.gro -pbc mol -ur compact) first. Lots of people have their own bilayer but they may be for different FFs which means the atom naming would not be immediately be compatible with your FF; for example mine are built for charmm36 and would require atom renaming for another FF, even charmm27. On 2012-05-26 11:24:12AM +0400, James Starlight wrote: Dear Gromacs Users! I want to perform MD simulation of my membrane protein in POPC or POPE bilayer using Tieleman's parameters for lipids by means of gromos united atom force field. The main problem is that the pre-equilibrated bilayers wich I found on the Dr. Tieleman's site consist of no more that 128 lipids but I want to simulate my protein with bigger number of lipids ( for example starting from 200 lipids ). What should I do in that case ? Could you provide me with some tools for construction of such united-atoms bilayers with desired dimensions ? Finally is there any others pre-equilibrated bilayers aviable for downloading besides Dr. Tieleman's site ? thanks for your help, James S. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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
