Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle!
Dear Andre, Rajat, Stephane, Patrick Justin, Dear Vesicle Simulators! Thank your for all your clues, we really appreciate them and they helped us to solve our problem! Some weeks ago, I asked you about my problem while simulating a vesicle using united-atoms method (ffG45a3). The main problem was the forming of a vacuum in the internal side of the vescile when I started the equillibration after removing water out of the membrane. The vacuum bubble was created because the lipid packing was too dense, which resulted in a relaxation of the vesicle and a volume enlargement. I solved this problem and just wanted to tell you how I did this. First of all I removed, as you suggested, less water, by using my TCL script. The vaccum bubble was still created but I just used genbox a second time and equillibrated again, after this, no vacuum was found. (The repetition of the genbox might have to be repeated a second time, depending on the packing density.) The production run gave me no problems at all and my simulation worked out pretty well. I used some self-written python scripts to analyse the vesicle and found out it was relatively stable. Also, there is the TCL script which I used to remove the water from the vesicle membrane. If you're interested, you can find these scripts here: cellmicrocosmos.org/Cmforum/viewtopic.php?f=18t=762 (Please copy this link to your browser - I had some problems sending the email with the full URL to the user list.) We are happy about critics or suggestions for improvement of the scripts! Best wishes, Manuel and Björn P.S.: Some additional comments about your suggestions: we wanted to use a direct method, using the membrane model from the MembraneEditor and then just starting a MD simulation with ffG45a3. The idea with the pore and the MARTINI force field is very good and interesting, but would be too complicated for our purposes. Because time was limited for this project, we also skipped the (very interesting) idea with the surface tension computation, because the method and its implementation seems to be bit time-consuming. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle
Hi Björn, my five cents. Did you consider constructing the system using MARTINI, equilibrating it with artificial pores and then back-map it to all-atom? Otherwise, I guess this artificial pore strategy could be applied to an all-atom system, but it'd be way more lengthy. Ciao, Patrick Le 28/10/2014 12:32, Justin Lemkul a écrit : On 10/28/14 6:23 AM, Björn Sommer wrote: Dear Rajat, Dear Andre, Dear all, thanks again for your help. 1) I'm simulating an united atoms model and isotropic pressure is used, not coarse-grained (this would be indeed more simple, because faster and much more examples are available). 2) Yes, I added additional water bubbles of different sizes only in the vacuum region. 3) I don't know the lateral tension yet, but I'll try to compute it and hand in this information later. 4) Do you have sufficient water outside the vesicle to hydrate all the lipids in the outer leaflet? 4) Yes, there should be enough water. I think, that this is currently not the problem, but we will keep this in mind. In addition, you find two snapshots, one of the vacuum bubble and one of the inner lipid layer coated by water: http://www.CELLmicrocosmos.org/images/downloads/cm2/WANTED_vacuum_bubble.pdf (Sorry, I just had to do this joke, Manuel! - Björn ;-) In addition I'm running a minimization run right now with a lot more water inside and will continue to equillibrate soon, as far as I get an useful result, we will inform you. Does the size of the vesicle itself change at all? My thought is that this could simply be a force field issue; if the surface tension in the vesicle is wrong, then if it gets larger over time, there's only a finite amount of water in the center of the vesicle, so bubbles develop. Apologies if I've missed relevant information; I've been following the thread but have not had time to study it very closely. -Justin -- ___ Patrick FUCHS Dynamique des membranes et trafic intracellulaire Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris Tel : +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle
Dear Manuel/Björn, I think Patrick has a point, an artificial pore should allow the solvent to equilibrate itself across the bilayer, but you need to choose atomistic and coarse grained force fields that yield very close areas per lipid (for planar bilayers, for instance), otherwise the atomistic and coarse grained vesicles will most likely relax to different curvatures and lipid packing, and then the pore won't be much useful as a strategy to relax the pore, you will probably end up with the wrong hydration inside the vesicle (either too few or too many water molecules). best, Andre On Wed, Oct 29, 2014 at 6:32 AM, Patrick Fuchs patrick.fu...@univ-paris-diderot.fr wrote: Hi Björn, my five cents. Did you consider constructing the system using MARTINI, equilibrating it with artificial pores and then back-map it to all-atom? Otherwise, I guess this artificial pore strategy could be applied to an all-atom system, but it'd be way more lengthy. Ciao, Patrick Le 28/10/2014 12:32, Justin Lemkul a écrit : On 10/28/14 6:23 AM, Björn Sommer wrote: Dear Rajat, Dear Andre, Dear all, thanks again for your help. 1) I'm simulating an united atoms model and isotropic pressure is used, not coarse-grained (this would be indeed more simple, because faster and much more examples are available). 2) Yes, I added additional water bubbles of different sizes only in the vacuum region. 3) I don't know the lateral tension yet, but I'll try to compute it and hand in this information later. 4) Do you have sufficient water outside the vesicle to hydrate all the lipids in the outer leaflet? 4) Yes, there should be enough water. I think, that this is currently not the problem, but we will keep this in mind. In addition, you find two snapshots, one of the vacuum bubble and one of the inner lipid layer coated by water: http://www.CELLmicrocosmos.org/images/downloads/cm2/ WANTED_vacuum_bubble.pdf (Sorry, I just had to do this joke, Manuel! - Björn ;-) In addition I'm running a minimization run right now with a lot more water inside and will continue to equillibrate soon, as far as I get an useful result, we will inform you. Does the size of the vesicle itself change at all? My thought is that this could simply be a force field issue; if the surface tension in the vesicle is wrong, then if it gets larger over time, there's only a finite amount of water in the center of the vesicle, so bubbles develop. Apologies if I've missed relevant information; I've been following the thread but have not had time to study it very closely. -Justin -- ___ Patrick FUCHS Dynamique des membranes et trafic intracellulaire Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris Tel : +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle
Dear Rajat, Dear Andre, Dear all, thanks again for your help. 1) I'm simulating an united atoms model and isotropic pressure is used, not coarse-grained (this would be indeed more simple, because faster and much more examples are available). 2) Yes, I added additional water bubbles of different sizes only in the vacuum region. 3) I don't know the lateral tension yet, but I'll try to compute it and hand in this information later. 4) Do you have sufficient water outside the vesicle to hydrate all the lipids in the outer leaflet? 4) Yes, there should be enough water. I think, that this is currently not the problem, but we will keep this in mind. In addition, you find two snapshots, one of the vacuum bubble and one of the inner lipid layer coated by water: http://www.CELLmicrocosmos.org/images/downloads/cm2/WANTED_vacuum_bubble.pdf (Sorry, I just had to do this joke, Manuel! - Björn ;-) In addition I'm running a minimization run right now with a lot more water inside and will continue to equillibrate soon, as far as I get an useful result, we will inform you. Best wishes, Manuel and Björn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle
On 10/28/14 6:23 AM, Björn Sommer wrote: Dear Rajat, Dear Andre, Dear all, thanks again for your help. 1) I'm simulating an united atoms model and isotropic pressure is used, not coarse-grained (this would be indeed more simple, because faster and much more examples are available). 2) Yes, I added additional water bubbles of different sizes only in the vacuum region. 3) I don't know the lateral tension yet, but I'll try to compute it and hand in this information later. 4) Do you have sufficient water outside the vesicle to hydrate all the lipids in the outer leaflet? 4) Yes, there should be enough water. I think, that this is currently not the problem, but we will keep this in mind. In addition, you find two snapshots, one of the vacuum bubble and one of the inner lipid layer coated by water: http://www.CELLmicrocosmos.org/images/downloads/cm2/WANTED_vacuum_bubble.pdf (Sorry, I just had to do this joke, Manuel! - Björn ;-) In addition I'm running a minimization run right now with a lot more water inside and will continue to equillibrate soon, as far as I get an useful result, we will inform you. Does the size of the vesicle itself change at all? My thought is that this could simply be a force field issue; if the surface tension in the vesicle is wrong, then if it gets larger over time, there's only a finite amount of water in the center of the vesicle, so bubbles develop. Apologies if I've missed relevant information; I've been following the thread but have not had time to study it very closely. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Naughty Vacuum Bubble in our Vesicle!
Dear all, we are trying to simulate a vesicle in water using united-atoms (Gromos96/ffG45a3). The system was modelled with the VesicleBuilder and the MembraneEditor. So first the vesicle was built (with 3 components: 2 PC, 1 Chol), and then it was embedded in a water (spc216) box with genbox. The membrane-intersecting water was removed by a custom Python script in VMD. After the removel or the intersecting water, the water seems to be very well enclosed in the inner membrane, without intersecting water atoms and with only a little space between the inner head groups and the water. The system minimization in water (spc216) worked pretty well, but after NPT-equillibration I found a vacuum bubble in the intracellular room of the vesicle. I tried to do a NVT-equillibration before the NPT, which ended with the same result. Using different barostats (parrinello-rahman, Berendsen) and refcoord-scaling options could'nt change anything, too. To repair the vacuum I tried to manually insert some water using pymol, after equillibrating this system again, i got the same result with an even bigger bubble in the centre. Analysing my system with g_energy showed a volume increase about 400nm³, which is rawly 4% more than the volume of the starting system. The systems energy increased by 20 kJ/mol. Trying to simulate the vesicle with the vacuum bubble inside resulted in a deformed vesicle and an increased distance between the outer and the inner lipid layer. The NPT.mdp file I used is the following: ;** ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 5 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.6 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME rcoulomb_switch = 0.0 rcoulomb = 1.6 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths= rvdw_switch = 0.9 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = AllEnerPres ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; Groups to couple separately = ;TODO: für mehrere Lipidtypen anpassen tc-grps = CHO DPC DPE SOL ; Time constant (ps) and reference temperature (K) = ;TAUT tau_t= 0.1 0.1 0.1 0.1 ;REFT ref_t= 300 300 300 300 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = isotropic ;semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 4.0 4.0 compressibility = 3e-5 3e-5 ref_p= 1.0 1.0 refcoord-scaling = no ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 105 gen_seed = 473529 ; OPTIONS FOR BONDS = constraints = all-bonds fourierspacing = pme_order= 6 optimize_fft = yes ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 30 ;** Also, I tried to relax my vesicle under NPT in vacuum in order to add water in a later step, but the NPT ended with a lot of LINCS warning (rotation more than 30 degrees). Okay, we read already that there are some information in the gmx-list discussing this problem, but the question is if it basically makes sense to follow the idea of a vaccum simulation or if we should directly start with solvated system in any case. Can you suggest us any method to solve this problem or maybe help us to improve our .mdp? Would be great! Best wishes, Manuel (and Björn) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle!
Dear Manuel/Björn, you cannot ignore that vesicle-like structures have a complex interfacial energy, with terms arising from both the packing of lipids and the curvature of the interface, among other factors. If it happens that you placed the wrong number of water molecules inside the cavity, pressure coupling with ordinary pressure values cannot fix a vacuum bubble just like it would for an isotropic liquid, because the elimination of the bubble would then require that both lipid packing and interface curvature should change (your result clearly says that it is preferable to form a vacuum bubble than to shrink the vesicle itself - and this is not a simulation issue neither it is an artifact, this is just a balance between different surface energy contributions arising from the vacuum cavity and the vesicle interfaces). As I see it, you should try to remove fewer water molecules from the original cavity (maybe relaxing the distance criteria to remove an overlapping water molecule). I hope it helps. best, Andre On Mon, Oct 27, 2014 at 1:15 PM, Björn Sommer bjo...@cellmicrocosmos.org wrote: Dear all, we are trying to simulate a vesicle in water using united-atoms (Gromos96/ffG45a3). The system was modelled with the VesicleBuilder and the MembraneEditor. So first the vesicle was built (with 3 components: 2 PC, 1 Chol), and then it was embedded in a water (spc216) box with genbox. The membrane-intersecting water was removed by a custom Python script in VMD. After the removel or the intersecting water, the water seems to be very well enclosed in the inner membrane, without intersecting water atoms and with only a little space between the inner head groups and the water. The system minimization in water (spc216) worked pretty well, but after NPT-equillibration I found a vacuum bubble in the intracellular room of the vesicle. I tried to do a NVT-equillibration before the NPT, which ended with the same result. Using different barostats (parrinello-rahman, Berendsen) and refcoord-scaling options could'nt change anything, too. To repair the vacuum I tried to manually insert some water using pymol, after equillibrating this system again, i got the same result with an even bigger bubble in the centre. Analysing my system with g_energy showed a volume increase about 400nm³, which is rawly 4% more than the volume of the starting system. The systems energy increased by 20 kJ/mol. Trying to simulate the vesicle with the vacuum bubble inside resulted in a deformed vesicle and an increased distance between the outer and the inner lipid layer. The NPT.mdp file I used is the following: ;** ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 5 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.6 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME rcoulomb_switch = 0.0 rcoulomb = 1.6 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths= rvdw_switch = 0.9 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = AllEnerPres ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; Groups to couple separately = ;TODO: für mehrere Lipidtypen anpassen tc-grps = CHO DPC DPE SOL ; Time constant (ps) and reference temperature (K) = ;TAUT tau_t= 0.1 0.1 0.1 0.1 ;REFT ref_t= 300 300 300 300 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = isotropic ;semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 4.0 4.0 compressibility = 3e-5 3e-5 ref_p= 1.0 1.0 refcoord-scaling = no ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 105 gen_seed = 473529 ; OPTIONS FOR BONDS = constraints = all-bonds fourierspacing = pme_order= 6 optimize_fft = yes ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 30 ;** Also, I tried to relax my vesicle under NPT in vacuum in order to add water in a later
Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle!
Hi Bjorn, I agree with Andre. Pack more water molecules inside the vesicle than what you currently have. It is likely that the water penetrates quite a bit into the headgroups, and hence you need more waters than you think (since water can hydrogen bond with the lipid head groups). Also try warming the waters slowly with an SA protocol while restraining the lipids. Regards, On Monday, October 27, 2014, André Farias de Moura mo...@ufscar.br wrote: Dear Manuel/Björn, you cannot ignore that vesicle-like structures have a complex interfacial energy, with terms arising from both the packing of lipids and the curvature of the interface, among other factors. If it happens that you placed the wrong number of water molecules inside the cavity, pressure coupling with ordinary pressure values cannot fix a vacuum bubble just like it would for an isotropic liquid, because the elimination of the bubble would then require that both lipid packing and interface curvature should change (your result clearly says that it is preferable to form a vacuum bubble than to shrink the vesicle itself - and this is not a simulation issue neither it is an artifact, this is just a balance between different surface energy contributions arising from the vacuum cavity and the vesicle interfaces). As I see it, you should try to remove fewer water molecules from the original cavity (maybe relaxing the distance criteria to remove an overlapping water molecule). I hope it helps. best, Andre On Mon, Oct 27, 2014 at 1:15 PM, Björn Sommer bjo...@cellmicrocosmos.org javascript:; wrote: Dear all, we are trying to simulate a vesicle in water using united-atoms (Gromos96/ffG45a3). The system was modelled with the VesicleBuilder and the MembraneEditor. So first the vesicle was built (with 3 components: 2 PC, 1 Chol), and then it was embedded in a water (spc216) box with genbox. The membrane-intersecting water was removed by a custom Python script in VMD. After the removel or the intersecting water, the water seems to be very well enclosed in the inner membrane, without intersecting water atoms and with only a little space between the inner head groups and the water. The system minimization in water (spc216) worked pretty well, but after NPT-equillibration I found a vacuum bubble in the intracellular room of the vesicle. I tried to do a NVT-equillibration before the NPT, which ended with the same result. Using different barostats (parrinello-rahman, Berendsen) and refcoord-scaling options could'nt change anything, too. To repair the vacuum I tried to manually insert some water using pymol, after equillibrating this system again, i got the same result with an even bigger bubble in the centre. Analysing my system with g_energy showed a volume increase about 400nm³, which is rawly 4% more than the volume of the starting system. The systems energy increased by 20 kJ/mol. Trying to simulate the vesicle with the vacuum bubble inside resulted in a deformed vesicle and an increased distance between the outer and the inner lipid layer. The NPT.mdp file I used is the following: ;** ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 5 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.6 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = PME rcoulomb_switch = 0.0 rcoulomb = 1.6 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths= rvdw_switch = 0.9 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = AllEnerPres ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; Groups to couple separately = ;TODO: für mehrere Lipidtypen anpassen tc-grps = CHO DPC DPE SOL ; Time constant (ps) and reference temperature (K) = ;TAUT tau_t= 0.1 0.1 0.1 0.1 ;REFT ref_t= 300 300 300 300 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = isotropic ;semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 4.0 4.0 compressibility = 3e-5 3e-5 ref_p= 1.0 1.0 refcoord-scaling = no ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 105 gen_seed = 473529 ; OPTIONS FOR BONDS = constraints = all-bonds fourierspacing =
[gmx-users] Naughty Vacuum Bubble in our Vesicle
Hello Bjorn I don't know if it related to your problem, but I see a typo in our mdp file for the pressure coupling: Pcoupltype = isotropic ;semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 4.0 4.0 compressibility = 3e-5 3e-5 ref_p= 1.0 1.0 You should have only one value for tau_p, compressibility and ref_p if you want to use an isotropic pressure coupling scheme in simulation (and two in case of semiisotropic). Strange that grompp did not mention this error. HTH Stephane -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle
Dear Andre, Rajat Stephane, thanks a lot for your light-speed suggestions! @More Water Idea I'll try to remove as less water as possible in my next try. But, what bothers me is the fact, that I manually added some water after the vacuum bubble was formed and equillibrated again, which resulted in another vaccuum bubble with the same or even larger size! From my understanding, this should not happen. Maybe I overlooked something? @Typo in MDP Thanks Stephane. We used a number of MDPs, we first have to check them all, if the typo was only an exception or if it was repeated several times. But we will take this into account but I fear, this is not causing the vacuum bubble - but we will check it! By the way, we are using GMX 4.6.X - would it make sense to switch to GMX 5? Thanks a lot best wishes! Manuel Björn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle
Dear Bjorn, A few thoughts: 1) Are you simulating a coarse grained system (Martini) or an all-atom system. Isotropic pressure coupling may be more appropriate for a vesicle because of its spherical symmetry. 2) When you manually added water, did you do it in the vacuum bubble region only? 3) What is that lateral tension in your vesicle? If your initial vesicle is tightly packed and has a lot of tension, it may expand to relax, in which case the internal density of the water may decrease in your production simulations. (see the PNAS paper from Marrink's group for the procedure to compute lateral tension). 4) Do you have sufficient water outside the vesicle to hydrate all the lipids in the outer leaflet? How about attaching a few snapshots so that we may take a look at them? Regards, On Tuesday, October 28, 2014, Björn Sommer bjo...@cellmicrocosmos.org wrote: Dear Andre, Rajat Stephane, thanks a lot for your light-speed suggestions! @More Water Idea I'll try to remove as less water as possible in my next try. But, what bothers me is the fact, that I manually added some water after the vacuum bubble was formed and equillibrated again, which resulted in another vaccuum bubble with the same or even larger size! From my understanding, this should not happen. Maybe I overlooked something? @Typo in MDP Thanks Stephane. We used a number of MDPs, we first have to check them all, if the typo was only an exception or if it was repeated several times. But we will take this into account but I fear, this is not causing the vacuum bubble - but we will check it! By the way, we are using GMX 4.6.X - would it make sense to switch to GMX 5? Thanks a lot best wishes! Manuel Björn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle
Dear Manuel/Björn, based on your description, I guess that placing some more water after the bubble has formed may not work as expected, because the bilayer forming the vesicle might be somehow strained, that's why a suggested stepping back to the system before equilibration. I think the number of water molecules that fit inside a vesicle is a typical trial and error problem. and upgrading software doesn't seem to change anything, since this is related to the physics of the model, not to the computation itself. best, Andre On Mon, Oct 27, 2014 at 5:13 PM, Björn Sommer bjo...@cellmicrocosmos.org wrote: Dear Andre, Rajat Stephane, thanks a lot for your light-speed suggestions! @More Water Idea I'll try to remove as less water as possible in my next try. But, what bothers me is the fact, that I manually added some water after the vacuum bubble was formed and equillibrated again, which resulted in another vaccuum bubble with the same or even larger size! From my understanding, this should not happen. Maybe I overlooked something? @Typo in MDP Thanks Stephane. We used a number of MDPs, we first have to check them all, if the typo was only an exception or if it was repeated several times. But we will take this into account but I fear, this is not causing the vacuum bubble - but we will check it! By the way, we are using GMX 4.6.X - would it make sense to switch to GMX 5? Thanks a lot best wishes! Manuel Björn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
