[gmx-users] surface tension-crash at step 0
Hi all, I have problem ruunning NVT with Z direction extended to get surface tension of a polymer packed in a cell. I tried the same procedure for an alkane and NVT works well however for the polymer the run crashes at the very first step.. Doe anyone have clue what wrong could be? Many thanks. starting mdrun 'Polymer' 1000 steps, 1.0 ps. step 0 [node6:14338] *** Process received signal *** [node6:14339] *** Process received signal *** [node6:14338] Signal: Segmentation fault (11) [node6:14338] Signal code: Address not mapped (1) [node6:14338] Failing at address: 0x2fbbaca0 [node6:14339] Signal: Segmentation fault (11) [node6:14339] Signal code: Address not mapped (1) [node6:14339] Failing at address: 0x2fbbd2e0 [node6:14339] [ 0] /lib64/libpthread.so.0 [0x3112e0ebe0] [node6:14339] [ 1] /usr/local/gromacs/lib/libgmx_mpi.so.6 [0x2b2fd8203c54] [node6:14339] *** End of error message *** [node6:14338] [ 0] /lib64/libpthread.so.0 [0x3112e0ebe0] [node6:14338] [ 1] /usr/local/gromacs/lib/libgmx_mpi.so.6 [0x2b4b10e86c65] [node6:14338] *** End of error message *** -- mpirun noticed that process rank 3 with PID 14338 on node node6 exited on signal 11 (Segmentation fault). On 4 April 2013 12:59, André Farias de Moura mo...@ufscar.br wrote: just that simple: as soon as you expand the box in the z direction the systems releases the excess pressure by the expansion of the liquid into the evacuated region. On Thu, Apr 4, 2013 at 1:20 PM, Elisabeth katesed...@gmail.com wrote: Dear Dr. Moura, Thank you for your answer. I equilibrated the cell under NPT and then extended the Z direction to get a surface. Since I run NVT and Z is extended, I see no pressure dependence and surface tension values are similar for all P from 50 to 1000 bar. which is attributed to the fact that Z is extended and system tends to expand regardless of the pressure that was imposed in the initial NPT runs. I have no gas, it is liqiuid-vaccum and wanted to know if there is anyway to capture effect of pressure. From your answer I think there is no such possibility... Please comment if the answer is positive, Thank you On 4 April 2013 10:32, André Farias de Moura mo...@ufscar.br wrote: There's no simple answer for that. If you apply a lateral pressure (xy plane) and the system is evacuated in the z direction, the only thing that you might expect is that your system would be squeezed in that direction, and then the lateral pressure would relax. If you're thinking about a gas exerting a pressure on the interface, your system would need to have a pressurized gas instead of vacuum in the z direction. Please note that pressure would arise from the gas you have put into the box and not from an external pressure bath (I would stick to NVT for such a model). Among the possible issue you might face, the gas would probably be partially miscible in the liquid phase for high pressures. I hope it helps. cheers Andre On Wed, Apr 3, 2013 at 11:07 PM, Elisabeth katesed...@gmail.com wrote: Hello all, Does anyone know how one can study the effect of pressure on surface tension of pure liquids? Thanks, -- 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 -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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 -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] surface tension
There's no simple answer for that. If you apply a lateral pressure (xy plane) and the system is evacuated in the z direction, the only thing that you might expect is that your system would be squeezed in that direction, and then the lateral pressure would relax. If you're thinking about a gas exerting a pressure on the interface, your system would need to have a pressurized gas instead of vacuum in the z direction. Please note that pressure would arise from the gas you have put into the box and not from an external pressure bath (I would stick to NVT for such a model). Among the possible issue you might face, the gas would probably be partially miscible in the liquid phase for high pressures. I hope it helps. cheers Andre On Wed, Apr 3, 2013 at 11:07 PM, Elisabeth katesed...@gmail.com wrote: Hello all, Does anyone know how one can study the effect of pressure on surface tension of pure liquids? Thanks, -- 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 -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] surface tension
Dear Dr. Moura, Thank you for your answer. I equilibrated the cell under NPT and then extended the Z direction to get a surface. Since I run NVT and Z is extended, I see no pressure dependence and surface tension values are similar for all P from 50 to 1000 bar. which is attributed to the fact that Z is extended and system tends to expand regardless of the pressure that was imposed in the initial NPT runs. I have no gas, it is liqiuid-vaccum and wanted to know if there is anyway to capture effect of pressure. From your answer I think there is no such possibility... Please comment if the answer is positive, Thank you On 4 April 2013 10:32, André Farias de Moura mo...@ufscar.br wrote: There's no simple answer for that. If you apply a lateral pressure (xy plane) and the system is evacuated in the z direction, the only thing that you might expect is that your system would be squeezed in that direction, and then the lateral pressure would relax. If you're thinking about a gas exerting a pressure on the interface, your system would need to have a pressurized gas instead of vacuum in the z direction. Please note that pressure would arise from the gas you have put into the box and not from an external pressure bath (I would stick to NVT for such a model). Among the possible issue you might face, the gas would probably be partially miscible in the liquid phase for high pressures. I hope it helps. cheers Andre On Wed, Apr 3, 2013 at 11:07 PM, Elisabeth katesed...@gmail.com wrote: Hello all, Does anyone know how one can study the effect of pressure on surface tension of pure liquids? Thanks, -- 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 -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] surface tension
Hello all, Does anyone know how one can study the effect of pressure on surface tension of pure liquids? Thanks, -- 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] surface tension-density profile
Deal all, I am trying to build up my alkane system to calculate the surface tension a fixed pressure. Here are the steps: 1- First I did a 10 ns NPT to equilibrate the box and used the last frame gro and cpt file as input for the next step 2- I extended the box in Z to more than twice the initial box size and issued the following: grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v However, I am not clear about the setting of pressure coupling and compressibility. I guess I need to use 0 compressibility in Z with isotropic option? Please advise me on the settings and details of these calculations. I am going to compare the surface tension and density profiles at several different pressures. Thank you in advance :) Below is the md.mdp contents: pbc = xyz integrator = md dt = 0.001 nsteps = 2000 nstcomm = 100 ; Output control nstenergy = 100 nstxout = 100;1 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ; Neighbor searching nstlist = 10 ns_type = grid ; Electrostatics/VdW coulombtype = Shift vdw-type= Shift rcoulomb-switch = 1 rvdw-switch = 1 ;0.9 ; Cut-offs rlist = 1.35 rcoulomb= 1.1 ;1.1 rvdw= 1.1 Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 425 * * *Pcoupl = berendsen* *Pcoupltype = isotropic * *tau_p = 1 0.5* *compressibility = 3.5e-5 3.5e-5 0* *ref_p = 50 10** * gen_vel = no gen_temp= 500.0 gen_seed= 173529 constraints = none constraint-algorithm = lincs -- 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] surface tension, Long range LJ correction, TIP4P/2005
Hi All, I really need to know how to apply long range LJ correction to calculate surface tension of TIP4P/2005 water. I can get 65 dyn even i use vdw cut-off = 1.4 nm, but from the reference people can get 69 dyn. I included the LJ Long range LJ correction using the following .mdp, please note that i used: DispCorr = EnerPres, which means i included the long range LJ correction for energy and pressure, but why i can get only 65 dyn for surface tension. I can see Disper. corr. in the .log file, but i saw Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE I spend two weeks on this ,but still failed to know the reason, because only myself do MD in my department. Can anyone help?? title= Yo cpp = /usr/bin/cpp include = define = integrator = md tinit= 0 dt = 0.001 nsteps = 500 init_step= 0 comm-mode= Linear nstcomm = 1 comm-grps= bd-fric = 0 ld-seed = 1993 niter= 20 nstxout = 5000 nstvout = 8000 nstfout = 8000 nstcheckpoint= 1000 nstlog = 5000 nstenergy= 5000 nstxtcout= 500 xtc-precision= 1000 xtc-grps = energygrps = nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 implicit_solvent = No Tcoupl = v-rescale tc-grps = System tau_t= 0.1 ref_t= 300 Pcoupl = no Pcoupltype = isotropic tau_p= 1 compressibility = 4.5e-5 ref_p= 1.0 andersen_seed= 815131 annealing= no annealing_npoints= annealing_time = annealing_temp = gen_vel = yes gen_temp = 300 gen_seed = 1993 constraints = none constraint-algorithm = Lincs unconstrained-start = no Shake-SOR= no shake-tol= 1e-04 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 morse= no -- 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] surface tension, Long range LJ correction, TIP4P/2005
On 1/06/2012 12:18 AM, MD wrote: Hi All, I really need to know how to apply long range LJ correction to calculate surface tension of TIP4P/2005 water. I can get 65 dyn even i use vdw cut-off = 1.4 nm, but from the reference people can get 69 dyn. I included the LJ Long range LJ correction using the following .mdp, please note that i used: DispCorr = EnerPres, which means i included the long range LJ correction for energy and pressure, but why i can get only 65 dyn for surface tension. I can see Disper. corr. in the .log file, but i saw Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE That's normal for your choices of coulombtype and vdw-type. I spend two weeks on this ,but still failed to know the reason, because only myself do MD in my department. Can anyone help?? Yes. You can, by finding that 69 dyn reference and reading it :-) Nothing else is worthwhile. I'm now going to stop giving you the same advice each time you ask the same question. Mark title= Yo cpp nbsp; = /usr/bin/cpp include = define = integrator = md tinit= 0 dt = 0.001 nsteps = 500 init_step= 0 brcomm-mode= Linear nstcomm = 1 comm-grps= bd-fric = 0 ld-seed = 1993 niter= 20 nstxout = 5000 nstvout = 8000 nstfout nb sp; = 8000 nstcheckpoint= 1000 nstlog = 5000 nstenergy= 5000 nstxtcout= 500 xtc-precision= 1000 xtc-grps = energygrps = nstlist = 5 ns_type nbsp;= grid pbc = xyz rlist= 1.4 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0*rvdw = 1.4 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry nb sp;= 3d epsilon_surface = 0 optimize_fft = no gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 implicit_solvent = No Tcoupl = v-rescale tc-grps = System tau_t nbs p; = 0.1 ref_t= 300 Pcoupl = no Pcoupltype = isotropic tau_p= 1 compressibility = 4.5e-5 ref_p= 1.0 andersen_seed= 815131 annealing= no annealing_npoints = annealing_time = annealing_temp = gen_vel = yes gen_temp = 300 gen_seed = 1993 constraints = none constraint-algorithm = Lincs unconstrained-start = no Shake-SOR= no shake-tol= 1e-04 brlincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 morse= no * * * -- 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] Surface tension calculation of a bilayer with bilayer normal in y-direction
Dear gmx-users, I am pretty confused about how to calculate the surface tension of a bilayer which with its bilayer normal in y-direction rather than z-direction (as the default). How does the Surf*SurfTen option in g-energy work? Does it take z as a default bilayer normal? If so, how can I calculate the surface tension in my case? What if I use g_energy to get Pxx, Pyy and Pzz, than calculate my surface tension as: gamma= (Pyy - (Pxx+Pzz)/2) * Lz What exactly is the Lz? Is it the length of the bilayer normal or the length of either box-x or box-z (in my case are the bilayer plane). I will be vary thankful if anyone would kindly help me or discuss it with me. Thank you for your precious time. Joanne -- -- 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] surface tension of monolayer
Sriprajak Krongsuk wrote: Dear Users, I have perform the simulation of nonionic surfactant monolayer at the water-air interface. I started to run the system at the NPT-ensemble for 10 ns until it reached to an equilibrium. After that I continued to run it at the NVT-ensemble for 8 ns (4 ns for equilibrium and 4 ns for data collection). I have calculated the surface tension of the monolayer by using g_energy and it yielded about 23 mN/m which this value is close to an experimental data. However, I continued to run from the previous point for 4 ns and then performed the surface tension calculation again. At this point the surface tension is negative value (-17 mN/m). Again, I tried to continue to run it for 4 ns and I got the surface tension of 12 mN/m. Please define what previous point means. My question is why the average surface tension is too fluctuation? In my understanding if the system is in an equilibrium, the average surface tension should be nearly the same value. Any pressure-related quantity is subsequent to massive fluctuations, which will scale with system size. You usually need fairly long, robust simulations to obtain properly converged quantities. There is some discussion of this fact in relation to surface tension in the list archive. -Justin Please everyone suggest me how to handle such a problem. Thank you Dr. Sriprajak Krongsuk Physics Department, Faculty of Science Khon Kaen University, Thailand Tel. (Mobile) 081-2630095 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] surface tension vs. system size
Dear all, I performed surface tension calculations vs. different system size (NVT, mdp file is included at the end). The reported surface tension for hydrocarbon I am studying is 18 mN/m at 20C. I am getting ~ 175 bar nm from g_energy which means surface tension of around 9 mN/m. For box size 3 3 6 nm I get 202 bar nm which is 10 mN/m and is closer to the reported one. 0-Are my results reasonable? Is it possible to get closer to the actual surf. ten? or the current difference can not be improved by molecular dynamics? 1- I am just wondering how I can decide on the system size given runs performed (shown below). Which system I can stick to? 2- Can I conclude that surface tension I am getting is equilibrated one? RMSD is much larger than average!! There are 125 molecules in a 3 3 3 nm box initially. *F*or 6 6 ? runs: 3 3 3 was replicated in X and Y. (that is 4*125 molecules) *box size 6 6 18 nm (molecules fill up volume of 6 6 3 and Z direction is increased to 18 so total size is 6 6 18) * Statistics over 898601 steps [ *0. through 1797.2001 ps ]*, 1 data sets All statistics are over 898601 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen175.322.91813.06 -17.41 (kJ/mol) Statistics over 818001 steps [ *0. through 1636.0001 ps* ], 1 data sets All statistics are over 818001 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 175.4824.91814.64 -19.6398 (kJ/mol) Statistics over 569501 steps [ *500. through 1639.0001 ps* ], 1 data sets All statistics are over 569501 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 175.459 51815.85 -31.5002 (kJ/mol) Statistics over 321001 steps [* 1000.0001 through 1642.0001 ps ]*, 1 data sets All statistics are over 321001 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 168.1283.91812.23 -12.0096 (kJ/mol) *box size 6 6 8 nm. (molecules fill up volume of 6 6 3 and Z direction is increased to 8 so total size is 6 6 8) *Statistics over 101 steps [* 0. through 2000.0001 ps *], 1 data sets All statistics are over 101 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 177.2743.91819.27 -0.465725 (kJ/mol)* * Statistics over 750001 steps *[ 500. through 2000.0001 ps ],* 1 data sets All statistics are over 750001 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 176.2473.71817.8812.2119 (kJ/mol) * * - *box size 6 6 6 nm. (molecules fill up volume of 6 6 3 and Z direction is increased to 6 so total size is 6 6 6) *Statistics over 532601 steps [ 0. through 1065.2001 ps ], 1 data sets All statistics are over 532601 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 175.1372.21816.63 -2.51592 (kJ/mol) Statistics over 282601 steps [ *500. through 1065.2001 ps* ], 1 data sets All statistics are over 282601 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 178.4137.61815.25 -21.8612 (kJ/mol) - *box size 3 3 9 nm. (molecules fill up volume of 3 3 3 and Z direction is increased to 9 so total size is 3 3 9)* Statistics over 101 steps [ 0. through 2000.0001 ps ], 1 data sets All statistics are over 101 points Energy Average Err.Est. RMSD Tot-Drift --- #Surf*SurfTen 180.9858.23621.5518.4731 (kJ/mol) Statistics over 750001 steps [ 500. through 2000.0001 ps ], 1 data sets All statistics are over 750001
[gmx-users] surface tension
Hello, Thank you for your answer. 1- If I am right I have to increase the length in two directions rather than one, to create a plane parallel to XY for example? 2- Can you please give me an idea on how many molecules I need to have in the box and also what should be the thickness of layer? I have now 3nm X 9 X 9 dimensions. That is thickness of 3nm. What I did was replicating a 3nm box using genconf -nbox 3 3 1. I dont know what is the correct way of creating a layer for surface tension calculation. I appreciate any comments about number of molecules, box dimensions for such a study. 3- my last question is how can I make sure surface tension reported by g_energy is the equilibrated one. RMSD is very big compared to surf. ten. ! Thanks for your time. Elisabeth ** if you are interested in the surface tension of a pure liquid, which I assume is true from your message, then you need to create at least one surface, since periodic boundary conditions make the model system infinite, i.e., without a surface whatsoever. the easiest way to make that happen is to increase the length of the box in one direction, say the z direction. that way you will end up with a system that resemble a (thin) liquid film with vacuum below and above, meaning that you now have two surfaces. run a regular simulation (NVT) e use g_energy to get the surface tension. btw: as any other pressure related property, fluctuations are huge. best Andre On Wed, Mar 9, 2011 at 12:25 PM, Elisabeth katesed...@gmail.com wrote: Dear gmx users, Since I am new to surface tension topic I need to ask very trivial questions. Please help me out with these simple questions. As a starting point I am going to calculate surface tension of a pure alkane in a cubic box and compare with experimental values. 1- g_energy is giving #Surf*SurfTen by default. On the other hand surface tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e Pres-XX-(bar), Pres-YY(bar), Pres--(bar) Can anyone tell me what the difference between these two is? 2- In pressure coupling settings there is surface_tension option which I guess is applicable where surface tension needs to be kept fixed. If one want to calculate surface tension I dont think this option make sense. Am I right? 3- I am using the following setting: I calculate the average for a 2ns run and different start times as shown below. Although T, P and other quantities are equilibrated after 200ps, surface tension is not giving a constant value. Is that because I am not using berenden P coupling? (As mentioned in the manual surface tension works with berendsen) Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 1 compressibility = 4.5e-5 ref_p = 40 time period for which average is calculated Average RMSD Fluct. Drift Tot-Drift --- 1-2000 ps run: #Surf*SurfTen6.438443588.74 3588.35 0.091406182.721 500-2000 ps#Surf*SurfTen 12.85183605.72 3605.26 0.132126198.189 1000-2000ps #Surf*SurfTen18.88213610.97 3610.80.11819118.191 1500-2000ps #Surf*SurfTen 23.00723585.51 3584.93 -0.444037 -222.019 4- Assuming I am getting surface tension for a cubic box, to compare this with reported values in literature I need to divide by 6 (no. of surfaces)? 5- Does box six affect the results? (mine is 3.3 nm ). Thank you, -- 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] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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] Surface tension readings in NVT vs NPT simulations
David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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.se http://folding.bmc.uu.se -- gmx-users mailing list 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. 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] Surface tension readings in NVT vs NPT simulations
I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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 -- 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] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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 -- 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 -- 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
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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 -- 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 -- 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
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 16.59, Denny Frost wrote: Is that using anisotropic pressure coupling? yes. just try it On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto: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
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in the normal direction and to turn off dispersion corrections to the pressure. -- 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.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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 -- 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
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 17.17, Denny Frost wrote: Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? check manual. maybe there is only one tau_p value. Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net mailto:dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? Please be more specific. How do you do NPT simulations? This may influence the result. To get good result I would suggest to do pressure coupling only in
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
No, it requires six, acutally, for aniisotropic coupling. I decided to use semi-isotropic coupling with the xy compressibilities set to 4.5e-15 (it won't accept 0). This should keep the walls parallel to the z axis from moving and accomplish the same thing. Does this sound right? On Sat, Mar 12, 2011 at 9:24 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-03-12 17.17, Denny Frost wrote: Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? check manual. maybe there is only one tau_p value. Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net mailto:dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use such correction meaning that the property (say interfacial tension) is expected to deviate more from the experimental value? This indicates that the system behaves differently in comparison to the same simulation conducted with correction? Many thanks, Aldi On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 06.09, Denny Frost wrote: I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
On 2011-03-12 17.28, Denny Frost wrote: No, it requires six, acutally, for aniisotropic coupling. I decided to use semi-isotropic coupling with the xy compressibilities set to 4.5e-15 (it won't accept 0). This should keep the walls parallel to the z axis from moving and accomplish the same thing. Does this sound right? with semiisotropic you need only two values, with anisotropic either 3 or 6 values. Zero compressibility should work. On Sat, Mar 12, 2011 at 9:24 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 17.17, Denny Frost wrote: Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? check manual. maybe there is only one tau_p value. Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net mailto:dsfr...@cableone.net mailto:dsfr...@cableone.net mailto:dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as possible. Here we have more confidence that our molecules in systems behave accordingly judging from the macroscopic values we obtain. Meanwhile, in the NPAT calculation, we don't use
Re: [gmx-users] Surface tension readings in NVT vs NPT simulations
It won't take zero with the berendsen thermostat, but I only wish to do weak coupling for now. Yes, I only specified the two values for semiisotropic. What I'm asking is will this setup only do z-pressure coupling? On Sat, Mar 12, 2011 at 9:32 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-03-12 17.28, Denny Frost wrote: No, it requires six, acutally, for aniisotropic coupling. I decided to use semi-isotropic coupling with the xy compressibilities set to 4.5e-15 (it won't accept 0). This should keep the walls parallel to the z axis from moving and accomplish the same thing. Does this sound right? with semiisotropic you need only two values, with anisotropic either 3 or 6 values. Zero compressibility should work. On Sat, Mar 12, 2011 at 9:24 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 17.17, Denny Frost wrote: Thanks for answering that question about dispersion, that makes sense. Also, The values I currently get with NPT are around 58 mN/m, while the average values I get for NVT are around 16 mN/m, but with a variance of nearly 100% of that value. I'm beginning to see why you only do pressure coupling in the z direction, but gromacs 4.5.3 won't let you specify tau_p = 0. Any other way to do pressure coupling in just the z direction? check manual. maybe there is only one tau_p value. Denny On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost dsfr...@cableone.net mailto:dsfr...@cableone.net mailto:dsfr...@cableone.net mailto:dsfr...@cableone.net wrote: Is that using anisotropic pressure coupling? On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-03-12 16.45, Denny Frost wrote: I have run NPT simulations using isotropic and semiisotropic coupling with the same results. I have never done coupling in just one direction though, how do you do this?. I have never used Dispersion corrections. It seems to me that this would help, rather than hurt though since, as Aldi said, it will make the system closer to experimental values. I will give this a try and see what happens. My question still remains - why do NPT and NVT simulations give such different values for surface tension? Denny Frost You don't give any values so it is hard to judge. - NVT may have completely wrong pressure - Dispersion correction assumes a homogeneous system as regards the average disperson constant per volume, which you probably do not have. E.g. in an ice/water surface dispersion correction may induce melting. The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off. - Coupling in one direction: specify e.g. ref-p = 0 0 1 compressibility = 0 0 4e-5 tau_p = 0 0 5 On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com mailto:aldi.asm...@gmail.com wrote: David, I have a question that is still related to your reply. If the bulk liquid NPT and the interfacial liquid-vapor NVT simulations are performed using dispersion corrections to the pressure and energy, while the intefacial liquid-liquid NPAT simulation don't use any correction, can we say that all results are valid since we don't give the same treatment for all systems? In the NPT and NVT calculations, we apply corrections in order to reduce the discrepancy between the calculated and experimental properties (say density and surface tension) as small as
[gmx-users] Surface tension readings in NVT vs NPT simulations
I am running MD simulations on Liquid/Liquid interfaces and measuring the interfacial tension between them. I have found that the readings in NVT simulations are close to experimental values, but have a lot of variation. I run NPT simulations on the exact same system and find the results show very little variation, but the values are far from experimental results. Does anyone know why this happens? -- 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] surface tension in gmx
Dear gmx users, Since I am new to surface tension topic I need to ask very trivial questions. Please help me out with these simple questions. As a starting point I am going to calculate surface tension of a pure alkane in a cubic box and compare with experimental values. 1- g_energy is giving #Surf*SurfTen by default. On the other hand surface tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e Pres-XX-(bar), Pres-YY(bar), Pres--(bar) Can anyone tell me what the difference between these two is? 2- In pressure coupling settings there is surface_tension option which I guess is applicable where surface tension needs to be kept fixed. If one want to calculate surface tension I dont think this option make sense. Am I right? 3- I am using the following setting: I calculate the average for a 2ns run and different start times as shown below. Although T, P and other quantities are equilibrated after 200ps, surface tension is not giving a constant value. Is that because I am not using berenden P coupling? (As mentioned in the manual surface tension works with berendsen) Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 1 compressibility = 4.5e-5 ref_p = 40 time period for which average is calculated Average RMSD Fluct. Drift Tot-Drift --- 1-2000 ps run: #Surf*SurfTen6.438443588.74 3588.35 0.091406182.721 500-2000 ps#Surf*SurfTen 12.85183605.72 3605.26 0.132126198.189 1000-2000ps #Surf*SurfTen18.88213610.97 3610.80.11819118.191 1500-2000ps #Surf*SurfTen 23.00723585.51 3584.93 -0.444037 -222.019 4- Assuming I am getting surface tension for a cubic box, to compare this with reported values in literature I need to divide by 6 (no. of surfaces)? 5- Does box six affect the results? (mine is 3.3 nm ). Thank you, -- 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] surface tension in gmx
if you are interested in the surface tension of a pure liquid, which I assume is true from your message, then you need to create at least one surface, since periodic boundary conditions make the model system infinite, i.e., without a surface whatsoever. the easiest way to make that happen is to increase the length of the box in one direction, say the z direction. that way you will end up with a system that resemble a (thin) liquid film with vacuum below and above, meaning that you now have two surfaces. run a regular simulation (NVT) e use g_energy to get the surface tension. btw: as any other pressure related property, fluctuations are huge. best Andre On Wed, Mar 9, 2011 at 12:25 PM, Elisabeth katesed...@gmail.com wrote: Dear gmx users, Since I am new to surface tension topic I need to ask very trivial questions. Please help me out with these simple questions. As a starting point I am going to calculate surface tension of a pure alkane in a cubic box and compare with experimental values. 1- g_energy is giving #Surf*SurfTen by default. On the other hand surface tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e Pres-XX-(bar), Pres-YY(bar), Pres--(bar) Can anyone tell me what the difference between these two is? 2- In pressure coupling settings there is surface_tension option which I guess is applicable where surface tension needs to be kept fixed. If one want to calculate surface tension I dont think this option make sense. Am I right? 3- I am using the following setting: I calculate the average for a 2ns run and different start times as shown below. Although T, P and other quantities are equilibrated after 200ps, surface tension is not giving a constant value. Is that because I am not using berenden P coupling? (As mentioned in the manual surface tension works with berendsen) Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 1 compressibility = 4.5e-5 ref_p = 40 time period for which average is calculated Average RMSD Fluct. Drift Tot-Drift --- 1-2000 ps run: #Surf*SurfTen 6.43844 3588.74 3588.35 0.091406 182.721 500-2000 ps #Surf*SurfTen 12.8518 3605.72 3605.26 0.132126 198.189 1000-2000ps #Surf*SurfTen 18.8821 3610.97 3610.8 0.11819 118.191 1500-2000ps #Surf*SurfTen 23.0072 3585.51 3584.93 -0.444037 -222.019 4- Assuming I am getting surface tension for a cubic box, to compare this with reported values in literature I need to divide by 6 (no. of surfaces)? 5- Does box six affect the results? (mine is 3.3 nm ). Thank you, -- gmx-users mailing list 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. 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] surface tension in gmx
Hi, 1- g_energy is giving #Surf*SurfTen by default. On the other hand surface tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e Pres-XX-(bar), Pres-YY(bar), Pres--(bar) Can anyone tell me what the difference between these two is? They should be equal, bearing in mind units conversion. 2- In pressure coupling settings there is surface_tension option which I guess is applicable where surface tension needs to be kept fixed. If one want to calculate surface tension I dont think this option make sense. Am I right? Yes. 3- I am using the following setting: I calculate the average for a 2ns run and different start times as shown below. Although T, P and other quantities are equilibrated after 200ps, surface tension is not giving a constant value. Is that because I am not using berenden P coupling? (As mentioned in the manual surface tension works with berendsen) Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 1 compressibility = 4.5e-5 ref_p = 40 time period for which average is calculated Average RMSD Fluct. Drift Tot-Drift --- 1-2000 ps run: #Surf*SurfTen6.438443588.74 3588.35 0.091406182.721 500-2000 ps#Surf*SurfTen 12.85183605.72 3605.26 0.132126198.189 1000-2000ps #Surf*SurfTen18.88213610.97 3610.80.11819118.191 1500-2000ps #Surf*SurfTen 23.00723585.51 3584.93 -0.444037 -222.019 This question is anything but trivial! Look at the RMSD values compared with the averages. The dispersion is so high that you can't be sure if this is or not equilibrated. 4- Assuming I am getting surface tension for a cubic box, to compare this with reported values in literature I need to divide by 6 (no. of surfaces)? No. You have to divide by the number of interfaces (2 for a bilayer immersed in water, for instance) 5- Does box six affect the results? (mine is 3.3 nm ). Yes, but see answer 3, above. Thank you, -- 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] surface tension in gmx
regarding your first question, the definition of gamma is not correct, you are getting energy/length⁴ instead of energy/area (multiply by Lz instead of dividing by it) 2011/3/9 Pedro Alexandre de Araújo Gomes Lapido Loureiro palap...@gmail.com: Hi, 1- g_energy is giving #Surf*SurfTen by default. On the other hand surface tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e Pres-XX-(bar), Pres-YY(bar), Pres--(bar) Can anyone tell me what the difference between these two is? They should be equal, bearing in mind units conversion. 2- In pressure coupling settings there is surface_tension option which I guess is applicable where surface tension needs to be kept fixed. If one want to calculate surface tension I dont think this option make sense. Am I right? Yes. 3- I am using the following setting: I calculate the average for a 2ns run and different start times as shown below. Although T, P and other quantities are equilibrated after 200ps, surface tension is not giving a constant value. Is that because I am not using berenden P coupling? (As mentioned in the manual surface tension works with berendsen) Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 1 compressibility = 4.5e-5 ref_p = 40 time period for which average is calculated Average RMSD Fluct. Drift Tot-Drift --- 1-2000 ps run: #Surf*SurfTen 6.43844 3588.74 3588.35 0.091406 182.721 500-2000 ps #Surf*SurfTen 12.8518 3605.72 3605.26 0.132126 198.189 1000-2000ps #Surf*SurfTen 18.8821 3610.97 3610.8 0.11819 118.191 1500-2000ps #Surf*SurfTen 23.0072 3585.51 3584.93 -0.444037 -222.019 This question is anything but trivial! Look at the RMSD values compared with the averages. The dispersion is so high that you can't be sure if this is or not equilibrated. 4- Assuming I am getting surface tension for a cubic box, to compare this with reported values in literature I need to divide by 6 (no. of surfaces)? No. You have to divide by the number of interfaces (2 for a bilayer immersed in water, for instance) 5- Does box six affect the results? (mine is 3.3 nm ). Yes, but see answer 3, above. Thank you, -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list 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. 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] surface tension calcualtion
Hi all, Can someone comment if the method I am following is correct: I want to calculate surface tension of a liquid, I simulate a thin film of the liquid periodic in x-y and I expand the z periodic boundaries. Then I use g_energy (surface tension) to calculate the value and divide it with 2 as there are two surfaces. - Rohit -- 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] Surface tension coupling
Hi, I am trying to obtain the surface tension for the hexane-water interface. I used Gromacs 4.0.7. A simulation where I keep the X-Y dimensions fixed and let z fluctuate yields the following output: Energy Average RMSD Fluct. Drift Tot-Drift --- Box-X 8 0 0 0 0 Box-Y 8 0 0 0 0 Box-Z 9.90151 0.00902362 0.00902139 1.00596e-07 0.000694869 Volume 633.697 0.577512 0.577369 6.43816e-06 0.0444716 Density (SI)790.105 0.7201080.71993 -8.03015e-06 -0.0554683 Pres-XX (bar) -93.007111.668111.668 -5.85703e-05 -0.404574 Pres-YY (bar) -93.8345111.464111.461 -0.000388743 -2.68524 Pres-ZZ (bar) 1.04823102.795102.795 7.14103e-05 0.493267 #Surf*SurfTen 935.4151174.751174.74 0.0029272720.2201 In order to test this value, I have done a constant surface simulation. I expect that this run should also give me a stable system. In this case I set the X-Y dimensions free, fixed the Z dimension by setting the compressibility to zero. I set the surface tension to 935, which I obtained from the first simulation. This simulation yields completely bizarre results: Energy Average RMSD Fluct. Drift Tot-Drift --- Box-X 7.22688 0.478216 0.0850938 -0.00115819 -1.63015 Box-Y 7.22688 0.478216 0.0850938 -0.00115819 -1.63015 Box-Z 9.90248 0 0 0 0 Volume 519.44968.669612.4766 -0.166195 -233.919 Density (SI)980.851128.88823.3119 0.311983439.117 Pres-XX (bar) 8178.747814.172469.2518.246625682.1 Pres-YY (bar) 8189.387827.512458.45 18.2925743.2 Pres-ZZ (bar) 8284.247819.63 2462.718.266125709.6 #Surf*SurfTen 992.0221516.441516.41 -0.0216172 -30.4263 The section from the .mdp file I used is as follows: ; Pressure coupling is on Pcoupl = berendsen tau_p = 1.0 1.0 Pcoupltype = surface-tension compressibility = 4.5e-5 0 ref_p = 935.605 1.0 Some how, the system shrinks in X-Y dimensions rather than expand, and this yields strange pressure values. I does maintain the target surface-tension more or less, but the density is completely unrealistic. I also tested letting the z-dimension also free, which gave more reasonable results. The options are set to: ; Pressure coupling is on Pcoupl = berendsen tau_p = 1.0 1.0 Pcoupltype = surface-tension compressibility = 4.5e-5 4.5e-5 ref_p = 935.605 1.0 Energy Average RMSD Fluct. Drift Tot-Drift --- Box-X 7.88739 0.0533823 0.0365402 -0.000116266 -0.134811 Box-Y 7.88739 0.0533823 0.0365402 -0.000116266 -0.134811 Box-Z 10.18380.13604 0.0933104 0.000295756 0.342929 Volume 633.4620.92414 0.917408 -0.000332644 -0.385701 Density (SI)790.3981.152661.14426 0.000414983 0.481174 Pres-XX (bar) -90.6569 105.24105.186 0.01009911.7098 Pres-YY (bar) -91.2499104.286104.267 0.005885576.82433 Pres-ZZ (bar) 1.7982295.696295.6725 0.006364557.37971 #Surf*SurfTen 944.3441095.81 1095.8 0.01078612.5064 However in this case also the system does not seem to be stable, but slowly the z dimension increases. Any ideas? Am I doing a mistake in the .mdp file, or is there a problem with the surface tension coupling? Thanks in advance, Mehmet -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] surface tension calculation in g_energy
Hi all, I use the option #Surf*SurfTens in g_engery to calculate the surface tension, but I find that I really do not know how it works after I get some inconsistent results compared with the calculation using the formula gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz ( there are two surfaces here and the surfaces in normal to the Z-axis). Energy Average RMSD Fluct. Drift Tot-Drift --- #Surf*SurfTen1136.52557.05 2557 0.00852598 51.1559 == ### == A V E R A G E S == ### == Pressure (bar) -1.93061e+02 -6.88599e-01 -1.66823e-02 -6.84564e-01 -1.93953e+02 -2.93803e-02 7.79006e-03 -6.97915e-03 -9.87987e+01 The #Surf*SurfTens gives a value 568.25 bar*nm, and gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz gives a value 473.54 bar*nm. Please give me some suggestions about the inconsistency. Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] surface tension calculation in g_energy
Bo Zhou wrote: Hi all, I use the option “#Surf*SurfTens” in g_engery to calculate the surface tension, but I find that I really do not know how it works after I get some inconsistent results compared with the calculation using the formula “gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz” ( there are two surfaces here and the surfaces in normal to the Z-axis). Energy Average RMSD Fluct. Drift Tot-Drift --- #Surf*SurfTen1136.52557.05 2557 0.00852598 51.1559 == ### == A V E R A G E S == ### == Pressure (bar) -1.93061e+02 -6.88599e-01 -1.66823e-02 -6.84564e-01 -1.93953e+02 -2.93803e-02 7.79006e-03 -6.97915e-03 -9.87987e+01 The “#Surf*SurfTens” gives a value 568.25 bar*nm, and “gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz” gives a value 473.54 bar*nm. Please give me some suggestions about the inconsistency. Thanks in advance. How did you calculate it? Did you divide the average pressures by the average box length? Or did you compute gamma for each step and average that (this is automatically done in the simulation and stored in the energy file). The two ways of computing are not the same. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Surface Tension units
Dear All, I have carried out an analysis of the surface tension value of a bilayer system. I wish to know what are the units of surface tension and is it calculated as per interface or for the entire bilayer (including two leaflets). waiting for the reply eagerly, Priyanka S. Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search http://search.yahoo.com/search?fr=oni_on_mailp=graduation+giftscs=bz ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Surface Tension units
Hi, the units are bar.nm (1 bar.nm = 0.1 dyn/cm). The reported values are for the entire bilayer. Cheers. Pedro. 2007/10/4, priyanka srivastava [EMAIL PROTECTED]: Dear All, I have carried out an analysis of the surface tension value of a bilayer system. I wish to know what are the units of surface tension and is it calculated as per interface or for the entire bilayer (including two leaflets). waiting for the reply eagerly, Priyanka S. Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search http://search.yahoo.com/search?fr=oni_on_mailp=graduation+giftscs=bz ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Surface Tension of a lipid bilayer
Hello, I have a question about calculating the surface tension for the water-lipid interface of a lipid bilayer. After an MD run, I can use my .edr file and g_energy to calculate the surface tension. I believe that the surface tension is calculated something like gamma = (Pzz-(Pxx+Pyy)/2)/L. I was wondering though, is the pressure tensor and hence surface tension calculated over the entire simulation box? I would assume so, since I did not specify any molecules. To find the water-lipid surface tension, would I not need to sum over only the molecules at the surface? Would this be do-able in Gromacs? Would I have to write something separate to do this? In my coordinate file, I have DPPC atoms, solvent atoms, and other atoms (those that make up the head group ie O,N etc.). Could I just make an index group that is not DPPC and not Solvent, and sum over those atoms? Thanks, Mike Tomasini ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] surface tension
Dear all, what is the unit of surface tension in gromacs analysis? Is it dyn/cm or N/m. As according to me it is coming out to be in terms of N/m but it is attached with a conversion factor of some powers of 10. Kindly guide me. If I am getting e.g. 930.002 as the surface tension then what are it's units? See section 2.2 of the manual. Surface tension isn't actually defined, but after you read that, you'll know which it is. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] surface tension
Dear all, what is the unit of surface tension in gromacs analysis? Is it dyn/cm or N/m. As according to me it is coming out to be in terms of N/m but it is attached with a conversion factor of some powers of 10. Kindly guide me. If I am getting e.g. 930.002 as the surface tension then what are it's units? regards, Pri... __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] surface tension
Hi Pri, Surface tension of 930.002 in gromacs units = 93.0002 mN/m or (dyn/cm) serge priyanka srivastava wrote: Dear all, what is the unit of surface tension in gromacs analysis? Is it dyn/cm or N/m. As according to me it is coming out to be in terms of N/m but it is attached with a conversion factor of some powers of 10. Kindly guide me. If I am getting e.g. 930.002 as the surface tension then what are it's units? regards, Pri... ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Surface Tension Calculation
write g_energy 6 0 enter the number 6 is just the corresponding to the surface tension, it can be any one. Quoting Dallas B. Warren [EMAIL PROTECTED]: I posted a question a few days ago regarding the calculation of the surface tension of a lipid bilayer in Gromacs. The response that I got was to use the option #Surf*SurfTens in g_energy. I am not really sure how to do this. I have looked at the g-energy file in Gromacs, and I don't see any option that is #Surf*SurfTens. Maybe the file name is wrong, or I am running an older version of Gromacs or something. Let me know if is there is a way to calculate the surface tension of a lipid bilayer within the Gromacs program, or if it is necessary for me to modify the code. (The more detailed the better. I am new to Gromacs) I case no-one else responds by the sound of it, whether the surf term is present within the energy file will depend on the type of pressure coupling you are using. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Surface Tension Calculation
I posted a question a few days ago regarding the calculation of the surface tension of a lipid bilayer in Gromacs. The response that I got was to use the option #Surf*SurfTens in g_energy. I am not really sure how to do this. I have looked at the g-energy file in Gromacs, and I don't see any option that is #Surf*SurfTens. Maybe the file name is wrong, or I am running an older version of Gromacs or something. Let me know if is there is a way to calculate the surface tension of a lipid bilayer within the Gromacs program, or if it is necessary for me to modify the code. (The more detailed the better. I am new to Gromacs) I case no-one else responds by the sound of it, whether the surf term is present within the energy file will depend on the type of pressure coupling you are using. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Surface Tension Calculation
toma0052 wrote: Hi, I posted a question a few days ago regarding the calculation of the surface tension of a lipid bilayer in Gromacs. The response that I got was to use the option #Surf*SurfTens in g_energy. I am not really sure how to do this. I have looked at the g-energy file in Gromacs, and I don't see any option that is #Surf*SurfTens. Maybe the file name is wrong, or I am running an older version of Gromacs or something. Let me know if is there is a way to calculate the surface tension of a lipid bilayer within the Gromacs program, or if it is necessary for me to modify the code. (The more detailed the better. I am new to Gromacs) yes, print the diagonal terms of the pressure tensor, and assuming you surface is normal to the Z-axis you have gamma = (Pzz - (Pxx+Pyy)/2) / Lz where Lz is the box length. If you have two surfaces you have to divide by two. Thanks, Mike Tomasini ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
