[gmx-users] Re: Water spreading on graphene!
Yes, the water droplet should remain a droplet on graphene. Since you have a droplet, I assume you have much vacuum in the system. I would not use PME for such system, but would rather compensate it by using larger cutoffs. If you need a simple advice, it is -- enlarge the box to avoid any interactions, which you would not have had in real experiment. I also expect a specific behavior, if your droplet is very small. Maybe, I would simulate this system without PBC at all. Dr. Vitaly Chaban I have a graphene like surface (carbons on a hexagonal lattice with zero partial charges and some LJ parameters) with a drop of water placed on it. In principle, this is a hydrophobic surface and the drop should remain a droplet on it. However, surprisingly I am seeing that the drop is spreading within a 1 ns of the simulation. In the past I have done some similar simulations (with a different structure but basically zero partial charge surface and LJ) on which the drop remains a drop. Does any body have any ideas of what I may be doing wrong? Pasted below is my mdp and top file. Briefly, I am doing NVT simulation, PME for electrostatics, TIP3P water model, the surface is frozen and intra-surface interactions are excluded, the cut-off distances are 1 nm, velocity rescale thermostat (I tried both with the entire system coupled to the same thermostat and with sheet and water being coupled to different thermostats). Any suggestions are welcome. My analysis suggests this comes from the long range electrostatics because we have tested the same thing in LAMMPS. When we turn off PPPM and use cut-off based Coulomb (~5 nm) in LAMMPS (yes now we have changed the software) we don't see the drop spreading. I have done so many simulations and to have this problem stumps me!! Thanks for being helpful always. -- 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] Re: Water spreading on graphene!
Dear David, Vitaly and all, Thanks for the thoughts/comments. There are no partial charges on the carbons in this sheet. (Sorry if there was any confusion about this). I used gromacs_4.5.5 version for these simulations. I also did increase the graphene sheet size to 10 nm x 10 nm and the box size to have 4142 water molecules. Initially the drop is placed about 3-4 nm away from the graphene sheet. In 600 ps the drop moves towards the sheet (forming something that looks like a pillar of water) and begins to spread on the sheet. The setup itself is placed in a 20 nm x 20 nm x 20 nm box. So both big sheet, and big box do not seem to help. The interesting part is I have another set of simulations with silica surface. The partial charges are turned off to make it hydrophobic. In this case the droplet remains a droplet. The mdp files are the same - I am using PME and NVT system with the drop and sheet coupled to different thermostats. The silica surface is frozen (so t_ref = 0 for the sheet). I have tested this system for gromacs 4.0.5, and 4.5.5. In both cases it remains a droplet. The only difference in the two is that in case of silica surface the surface is periodic, while graphene is a finite size sheet. Does this make such a big difference? Thoughts, comments, suggestions welcome! thanks all, Sapna On Sun, Apr 21, 2013 at 6:39 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: Yes, the water droplet should remain a droplet on graphene. Since you have a droplet, I assume you have much vacuum in the system. I would not use PME for such system, but would rather compensate it by using larger cutoffs. If you need a simple advice, it is -- enlarge the box to avoid any interactions, which you would not have had in real experiment. I also expect a specific behavior, if your droplet is very small. Maybe, I would simulate this system without PBC at all. Dr. Vitaly Chaban I have a graphene like surface (carbons on a hexagonal lattice with zero partial charges and some LJ parameters) with a drop of water placed on it. In principle, this is a hydrophobic surface and the drop should remain a droplet on it. However, surprisingly I am seeing that the drop is spreading within a 1 ns of the simulation. In the past I have done some similar simulations (with a different structure but basically zero partial charge surface and LJ) on which the drop remains a drop. Does any body have any ideas of what I may be doing wrong? Pasted below is my mdp and top file. Briefly, I am doing NVT simulation, PME for electrostatics, TIP3P water model, the surface is frozen and intra-surface interactions are excluded, the cut-off distances are 1 nm, velocity rescale thermostat (I tried both with the entire system coupled to the same thermostat and with sheet and water being coupled to different thermostats). Any suggestions are welcome. My analysis suggests this comes from the long range electrostatics because we have tested the same thing in LAMMPS. When we turn off PPPM and use cut-off based Coulomb (~5 nm) in LAMMPS (yes now we have changed the software) we don't see the drop spreading. I have done so many simulations and to have this problem stumps me!! Thanks for being helpful always. -- 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 -- Sapna Sarupria Assistant Professor Department of Chemical and Biomolecular Engineering 128 Earle Hall Clemson University Clemson, SC 29634 -- 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] Re: Water spreading on graphene!
On 2013-04-21 12:39, Dr. Vitaly Chaban wrote: Yes, the water droplet should remain a droplet on graphene. Since you have a droplet, I assume you have much vacuum in the system. I would not use PME for such system, but would rather compensate it by using larger cutoffs. It could be an artifact if the box dimension is small compared to the droplet (less than double the droplet size, make it at least three times the droplet). In principle PME should work though. Check the energy before and after the droplet spreads to see whether the energy goes down. If you need a simple advice, it is -- enlarge the box to avoid any interactions, which you would not have had in real experiment. Indeed. I also expect a specific behavior, if your droplet is very small. Maybe, I would simulate this system without PBC at all. Dr. Vitaly Chaban I have a graphene like surface (carbons on a hexagonal lattice with zero partial charges and some LJ parameters) with a drop of water placed on it. In principle, this is a hydrophobic surface and the drop should remain a droplet on it. However, surprisingly I am seeing that the drop is spreading within a 1 ns of the simulation. In the past I have done some similar simulations (with a different structure but basically zero partial charge surface and LJ) on which the drop remains a drop. Does any body have any ideas of what I may be doing wrong? Pasted below is my mdp and top file. Briefly, I am doing NVT simulation, PME for electrostatics, TIP3P water model, the surface is frozen and intra-surface interactions are excluded, the cut-off distances are 1 nm, velocity rescale thermostat (I tried both with the entire system coupled to the same thermostat and with sheet and water being coupled to different thermostats). Any suggestions are welcome. My analysis suggests this comes from the long range electrostatics because we have tested the same thing in LAMMPS. When we turn off PPPM and use cut-off based Coulomb (~5 nm) in LAMMPS (yes now we have changed the software) we don't see the drop spreading. I have done so many simulations and to have this problem stumps me!! Thanks for being helpful always. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.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
Re: [gmx-users] Re: Water spreading on graphene!
Dear David and all, Thanks for the suggestions! I did increase the box size to twice that of the sheet dimensions. The sheet is 10 x 10 nm^2 and now is place in the center of a 20 x 20 x 20 nm^3 box with the droplet size of about 5 nm (4142 water molecules). I still see the droplet spreading. I will check the energies and also attempt the simulation with the cut-off distances. May be that will help. However, in a silica surface with no surface charges the drop remains a drop (as expected). I use the same mdp files for both the simulations. Sapna On Sun, Apr 21, 2013 at 12:14 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-04-21 12:39, Dr. Vitaly Chaban wrote: Yes, the water droplet should remain a droplet on graphene. Since you have a droplet, I assume you have much vacuum in the system. I would not use PME for such system, but would rather compensate it by using larger cutoffs. It could be an artifact if the box dimension is small compared to the droplet (less than double the droplet size, make it at least three times the droplet). In principle PME should work though. Check the energy before and after the droplet spreads to see whether the energy goes down. If you need a simple advice, it is -- enlarge the box to avoid any interactions, which you would not have had in real experiment. Indeed. I also expect a specific behavior, if your droplet is very small. Maybe, I would simulate this system without PBC at all. Dr. Vitaly Chaban -- 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] Re: Water spreading on graphene!
On 2013-04-21 18:25, Sapna Sarupria wrote: Dear David and all, Thanks for the suggestions! I did increase the box size to twice that of the sheet dimensions. The sheet is 10 x 10 nm^2 and now is place in the center of a 20 x 20 x 20 nm^3 box with the droplet size of about 5 nm (4142 water molecules). I still see the droplet spreading. I will check the energies and also attempt the simulation with the cut-off distances. May be that will help. However, in a silica surface with no surface charges the drop remains a drop (as expected). I use the same mdp files for both the simulations. You did not explain the charges on graphene. Sapna On Sun, Apr 21, 2013 at 12:14 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-04-21 12:39, Dr. Vitaly Chaban wrote: Yes, the water droplet should remain a droplet on graphene. Since you have a droplet, I assume you have much vacuum in the system. I would not use PME for such system, but would rather compensate it by using larger cutoffs. It could be an artifact if the box dimension is small compared to the droplet (less than double the droplet size, make it at least three times the droplet). In principle PME should work though. Check the energy before and after the droplet spreads to see whether the energy goes down. If you need a simple advice, it is -- enlarge the box to avoid any interactions, which you would not have had in real experiment. Indeed. I also expect a specific behavior, if your droplet is very small. Maybe, I would simulate this system without PBC at all. Dr. Vitaly Chaban -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.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
Re: [gmx-users] Re: Water spreading on graphene!
Dear David, I apologize for the confusion. There are no partial charges on the graphene sheet . The only interactions between the sheet and water are from VdW interactions. To give some background: We were initially simulating graphene oxide with water which has partial charges. Then to test the effect of oxygens we retained the carbons and their partial charges, and simulated the system. As expected it was hydrophilic. Then we turned off all the partial charges to obtain a graphene sheet and tested the system. Unexpectedly, we still saw the drop spreading. That is how the whole mystery originated. I hope this clarifies things. Again, there are no partial charges on the graphene sheet. Sapna On Sun, Apr 21, 2013 at 1:23 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-04-21 18:25, Sapna Sarupria wrote: Dear David and all, Thanks for the suggestions! I did increase the box size to twice that of the sheet dimensions. The sheet is 10 x 10 nm^2 and now is place in the center of a 20 x 20 x 20 nm^3 box with the droplet size of about 5 nm (4142 water molecules). I still see the droplet spreading. I will check the energies and also attempt the simulation with the cut-off distances. May be that will help. However, in a silica surface with no surface charges the drop remains a drop (as expected). I use the same mdp files for both the simulations. You did not explain the charges on graphene. Sapna On Sun, Apr 21, 2013 at 12:14 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-04-21 12:39, Dr. Vitaly Chaban wrote: Yes, the water droplet should remain a droplet on graphene. Since you have a droplet, I assume you have much vacuum in the system. I would not use PME for such system, but would rather compensate it by using larger cutoffs. It could be an artifact if the box dimension is small compared to the droplet (less than double the droplet size, make it at least three times the droplet). In principle PME should work though. Check the energy before and after the droplet spreads to see whether the energy goes down. If you need a simple advice, it is -- enlarge the box to avoid any interactions, which you would not have had in real experiment. Indeed. I also expect a specific behavior, if your droplet is very small. Maybe, I would simulate this system without PBC at all. Dr. Vitaly Chaban -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Sapna Sarupria Assistant Professor Department of Chemical and Biomolecular Engineering 128 Earle Hall Clemson University Clemson, SC 29634 -- 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
