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 <evanwlo...@gmail.com> 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 <sptiw...@gmail.com> > 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 0.67 190.708 2.20173 > > (bar) > > > Pres-ZZ -31.7913 0.0072 262.697 -0.0293928 > > (bar) > > > #Surf*SurfTen 1151.56 6.5 1806.55 -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.