Re: [gmx-users] Cut-off radius larger than the box length for Deform option?
Any help will be greatly appreciated. Surya Prakash Tiwari On Thu, Nov 2, 2017 at 5:05 PM, Surya Prakash Tiwari wrote: > Dear Gromacs users, > > Why simulation doesn't crash when one of the box length gets smaller than > the 2*cut-off radius mentioned in the MDP file, while using the deform > option of Gromacs? > > I assume that there is some special provision for cut-off with deform > option. I tried looking into the source code, and found the *deform* function > in *mdlib/update.cpp*, however, I could not understand the code. > > Can someone please explain me how deform option works along with the > cut-off, which makes the simulation to not crash. > > Thanks. > > > Surya Prakash Tiwari > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Cut-off radius larger than the box length for Deform option?
Dear Gromacs users, Why simulation doesn't crash when one of the box length gets smaller than the 2*cut-off radius mentioned in the MDP file, while using the deform option of Gromacs? I assume that there is some special provision for cut-off with deform option. I tried looking into the source code, and found the *deform* function in *mdlib/update.cpp*, however, I could not understand the code. Can someone please explain me how deform option works along with the cut-off, which makes the simulation to not crash. Thanks. Surya Prakash Tiwari -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Negative pressure in an interface NVT simulation
Thanks a lot David. The paper you mentioned was very helpful. I have figured out the reason of me getting negative pressure in interface simulations. This might be helpful to other researchers. I was using dispersion correction DispCorr = EnerPres in my mdp file. When this term is on for pressure, Gromacs adds a constant term P_lr (eq. 4.175, gmx manual 5.1.3) to the pressure obtained from virial and kinetic energy (eq. 3.22). The final pressure obtained in this way is not accurate for vapor liquid interface simulations, because vapor-liquid system is not homogeneous, and the average dispersion constant calculated is not correct. Despite getting wrong pressures, one gets the accurate surface tension because dispersion corrections added to the pressure tensors (Pxx, Pyy, Pzz) gets cancelled out while calculating surface tension. Instead of using cutoff for Lennard-Jones potential, I used Lennard-Jones PME built in Gromacs and found the correct pressures. Thank you. Surya Prakash Tiwari On Thu, Sep 29, 2016 at 2:16 AM, David van der Spoel wrote: > On 27/09/16 16:02, Surya Prakash Tiwari wrote: > >> Hello again, >> >> Can someone take my question. You don't need to fully answer my question. >> If you could just show me the direction, that would be more than enough. >> >> This is as it should be. Your system has a surface tension as you see > that you can compare to experimental data if you wish. Since you have two > surfaces you have to divide the number by 2 and correct for units. > Check J. Chem. Theory Comput. 11 pp. 2938-2944 (2015) for an up to date > discussion of surface tensions in simulations. > > > > Thanks in advance. >> >> Surya Prakash Tiwari >> >> On Wed, Sep 21, 2016 at 12:11 PM, Surya Prakash Tiwari < >> sptiw...@gmail.com> >> wrote: >> >> Dear Gromacs users, >>> >>> I am doing a water liquid-gas interface simulation in NVT ensemble (at >>> 298 >>> K, 1000 SPC/E, box size is described in the end). The pressure calculated >>> (after equilibration) using gmx energy shows negative values: >>> >>> Energy Average Err.Est. RMSD Tot-Drift >>> >>> --- >>> Pressure -151.627 0.67190.7082.20173 >>> (bar) >>> Pres-ZZ-31.7913 0.0072262.697 -0.0293928 >>> (bar) >>> #Surf*SurfTen 1151.566.51806.55 -21.4399 >>> (bar >>> nm) >>> >>> Since liquid and gas phases are in equilibrium, shouldn't pressure (at >>> least Pzz) be equal to the saturation pressure of water. A large negative >>> value is not making sense. Can someone help me with understanding this. >>> One >>> of my colleagues used NAMD, and he said that he is getting the right >>> pressure for the interface system! >>> >>> Though the pressures, I am getting, are negative; calculated surface >>> tension value matches well with those available in the literature. It >>> seems >>> that something is getting cancelled out, and I am getting the correct >>> surface tension. Am I right? >>> >>> I tried to look how the pressure is calculated in Gromacs. >>> Mathematically, >>> my pressures are negative because the virial energies are larger in the >>> case of interface simulation compared to the case without interface, >>> other >>> parameters remain almost same. >>> >>> >>> The starting configuration for the NVT interface simulation was obtained >>> using the following procedure: >>> 1. 1000 water molecules were equilibrated using NPT ensemble (298 K, 1 >>> bar). >>> 2. Find the average box lengths using gmx energy tool. >>> 3. Obtain a gro trajectory file from the xtc/trr file using: >>> gmx trjconv -f md -s md.tpr -o conf.gro -pbc whole -b 1000 >>> 4. A snapshot configuration from the above gro file was chosen such that >>> its box lengths matches with the average box lengths obtained in step 2 >>> (to >>> get the pressure right). >>> 5. Double the Z length of the gro file obtained in step 4. Use this as >>> the >>> starting configuration for NVT interface simulation. >>> >>> >>> I have tried to explain as much as possible to get the help, but if I am >>> missing some information, please let me know and I will provide that. >>> >>> >>> Thanks a lot. I look forward for some help. >>>
Re: [gmx-users] Negative pressure in an interface NVT simulation
Hi Evan, Thanks for answering. I ran for pretty long- 30 ns. I am sure that my system has reached equilibrium. This is evident from the very small values of Err.Est. and Tot-Drift of the pressure values included in my original question. Any other hint! Thanks. On Tue, Sep 27, 2016 at 3:36 PM, Evan Lowry wrote: > How long is your simulation? Is it possible that it has not reached > equilibrium yet? > > Evan L. > > On Tue, Sep 27, 2016 at 8:02 AM, Surya Prakash Tiwari > wrote: > > > Hello again, > > > > Can someone take my question. You don't need to fully answer my question. > > If you could just show me the direction, that would be more than enough. > > > > Thanks in advance. > > > > Surya Prakash Tiwari > > > > On Wed, Sep 21, 2016 at 12:11 PM, Surya Prakash Tiwari < > sptiw...@gmail.com > > > > > wrote: > > > > > Dear Gromacs users, > > > > > > I am doing a water liquid-gas interface simulation in NVT ensemble (at > > 298 > > > K, 1000 SPC/E, box size is described in the end). The pressure > calculated > > > (after equilibration) using gmx energy shows negative values: > > > > > > Energy Average Err.Est. RMSD Tot-Drift > > > > > > --- > > > Pressure -151.627 0.67190.7082.20173 > > (bar) > > > Pres-ZZ-31.7913 0.0072262.697 -0.0293928 > > (bar) > > > #Surf*SurfTen 1151.566.51806.55 -21.4399 > > (bar > > > nm) > > > > > > Since liquid and gas phases are in equilibrium, shouldn't pressure (at > > > least Pzz) be equal to the saturation pressure of water. A large > negative > > > value is not making sense. Can someone help me with understanding this. > > One > > > of my colleagues used NAMD, and he said that he is getting the right > > > pressure for the interface system! > > > > > > Though the pressures, I am getting, are negative; calculated surface > > > tension value matches well with those available in the literature. It > > seems > > > that something is getting cancelled out, and I am getting the correct > > > surface tension. Am I right? > > > > > > I tried to look how the pressure is calculated in Gromacs. > > Mathematically, > > > my pressures are negative because the virial energies are larger in the > > > case of interface simulation compared to the case without interface, > > other > > > parameters remain almost same. > > > > > > > > > The starting configuration for the NVT interface simulation was > obtained > > > using the following procedure: > > > 1. 1000 water molecules were equilibrated using NPT ensemble (298 K, 1 > > > bar). > > > 2. Find the average box lengths using gmx energy tool. > > > 3. Obtain a gro trajectory file from the xtc/trr file using: > > > gmx trjconv -f md -s md.tpr -o conf.gro -pbc whole -b 1000 > > > 4. A snapshot configuration from the above gro file was chosen such > that > > > its box lengths matches with the average box lengths obtained in step 2 > > (to > > > get the pressure right). > > > 5. Double the Z length of the gro file obtained in step 4. Use this as > > the > > > starting configuration for NVT interface simulation. > > > > > > > > > I have tried to explain as much as possible to get the help, but if I > am > > > missing some information, please let me know and I will provide that. > > > > > > > > > Thanks a lot. I look forward for some help. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Negative pressure in an interface NVT simulation
Hello again, Can someone take my question. You don't need to fully answer my question. If you could just show me the direction, that would be more than enough. Thanks in advance. Surya Prakash Tiwari On Wed, Sep 21, 2016 at 12:11 PM, Surya Prakash Tiwari wrote: > Dear Gromacs users, > > I am doing a water liquid-gas interface simulation in NVT ensemble (at 298 > K, 1000 SPC/E, box size is described in the end). The pressure calculated > (after equilibration) using gmx energy shows negative values: > > Energy Average Err.Est. RMSD Tot-Drift > > --- > Pressure -151.627 0.67190.7082.20173 (bar) > Pres-ZZ-31.7913 0.0072262.697 -0.0293928 (bar) > #Surf*SurfTen 1151.566.51806.55 -21.4399 (bar > nm) > > Since liquid and gas phases are in equilibrium, shouldn't pressure (at > least Pzz) be equal to the saturation pressure of water. A large negative > value is not making sense. Can someone help me with understanding this. One > of my colleagues used NAMD, and he said that he is getting the right > pressure for the interface system! > > Though the pressures, I am getting, are negative; calculated surface > tension value matches well with those available in the literature. It seems > that something is getting cancelled out, and I am getting the correct > surface tension. Am I right? > > I tried to look how the pressure is calculated in Gromacs. Mathematically, > my pressures are negative because the virial energies are larger in the > case of interface simulation compared to the case without interface, other > parameters remain almost same. > > > The starting configuration for the NVT interface simulation was obtained > using the following procedure: > 1. 1000 water molecules were equilibrated using NPT ensemble (298 K, 1 > bar). > 2. Find the average box lengths using gmx energy tool. > 3. Obtain a gro trajectory file from the xtc/trr file using: > gmx trjconv -f md -s md.tpr -o conf.gro -pbc whole -b 1000 > 4. A snapshot configuration from the above gro file was chosen such that > its box lengths matches with the average box lengths obtained in step 2 (to > get the pressure right). > 5. Double the Z length of the gro file obtained in step 4. Use this as the > starting configuration for NVT interface simulation. > > > I have tried to explain as much as possible to get the help, but if I am > missing some information, please let me know and I will provide that. > > > Thanks a lot. I look forward for some help. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] What is the meaning of negative surface tension?
What are the uncertainties in your pressure values? Sent from my phone On Sep 23, 2016 12:01 PM, "gozde ergin" wrote: > Also when I check the pressure in X,Y and Z axis, > Pzz = -0.34 bar > Pyy = -1275 bar > Pxx = 32 bar. > Pyy and Pxx should be equal to each other. So basically system is not > under equilibrium conditions. > How should I solve this problem? Any idea? > > > On 23 Sep 2016, at 09:27, gozde ergin wrote: > > > > Dear all, > > > > I am simulating organic covered salty water system in order to estimate > the surface tension. Force field is Charmm36 and water model in TIP3P. > > Surface tension is -127 mN/m after 5 ns run. What is the meaning of > negative surface tension? > > I was expecting +30 ~ +40 mN/m but not negative. > > Maybe my system was not under equilibrium conditions. > > Will longer running solve the problem? Any help would be appreciated. > > > > Thanks in advance. > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Negative pressure in an interface NVT simulation
Dear Gromacs users, I am doing a water liquid-gas interface simulation in NVT ensemble (at 298 K, 1000 SPC/E, box size is described in the end). The pressure calculated (after equilibration) using gmx energy shows negative values: Energy Average Err.Est. RMSD Tot-Drift --- Pressure -151.627 0.67190.7082.20173 (bar) Pres-ZZ-31.7913 0.0072262.697 -0.0293928 (bar) #Surf*SurfTen 1151.566.51806.55 -21.4399 (bar nm) Since liquid and gas phases are in equilibrium, shouldn't pressure (at least Pzz) be equal to the saturation pressure of water. A large negative value is not making sense. Can someone help me with understanding this. One of my colleagues used NAMD, and he said that he is getting the right pressure for the interface system! Though the pressures, I am getting, are negative; calculated surface tension value matches well with those available in the literature. It seems that something is getting cancelled out, and I am getting the correct surface tension. Am I right? I tried to look how the pressure is calculated in Gromacs. Mathematically, my pressures are negative because the virial energies are larger in the case of interface simulation compared to the case without interface, other parameters remain almost same. The starting configuration for the NVT interface simulation was obtained using the following procedure: 1. 1000 water molecules were equilibrated using NPT ensemble (298 K, 1 bar). 2. Find the average box lengths using gmx energy tool. 3. Obtain a gro trajectory file from the xtc/trr file using: gmx trjconv -f md -s md.tpr -o conf.gro -pbc whole -b 1000 4. A snapshot configuration from the above gro file was chosen such that its box lengths matches with the average box lengths obtained in step 2 (to get the pressure right). 5. Double the Z length of the gro file obtained in step 4. Use this as the starting configuration for NVT interface simulation. I have tried to explain as much as possible to get the help, but if I am missing some information, please let me know and I will provide that. Thanks a lot. I look forward for some help. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
?? Surya Prakash Tiwari On Thu, Nov 14, 2013 at 7:12 AM, Raj K wrote: > -- > Rajesh Kumar Kesharwani C/O Prof Krishna misra > > M.Tech (Bioinformatics) > Indian Institute of Information Technology-Allahabad > Contact: +919335323082 > -- > gromacs.org_gmx-users mailing list > gromacs.org_gmx-users@maillist.sys.kth.se > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_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 > -- gromacs.org_gmx-users mailing listgromacs.org_gmx-users@maillist.sys.kth.se https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_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
