Re: [gmx-users] (no subject)

Could you paste your .top file and the command your add ions? Maybe the Cl- ion was also added when you added Na+ ion? On Tue, Jun 12, 2012 at 1:18 PM, tarak karmakar wrote: > Dear All , > > I am facing problem in matching the coordinates number in this two files, > em.gro and toplogy.top. > I ha

Re: [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?

Dear Chris Thanks again for your reply. On Sat, Jun 2, 2012 at 10:52 PM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote: > I suspect that you can find an equation to relate the surface tension to > the ratio of the pressure along z to the pressure along xy that is required > to maintai

Re: [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?

Sorry for my carelessness. Before nose-hoover, Parrinello-Rahman, I have done v-rescale, berendsen already. tau_t = 0.1, tau_p = 0.5. Hugh. On Sat, Jun 2, 2012 at 12:43 PM, Mark Abraham wrote: > On 2/06/2012 1:11 PM, Klniu wrote: > > Dear Gromacs users, > > I am doing a memb

[gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?

Dear Gromacs users, I am doing a membrane simulation. The system are two layers composed by surfactants. other molecule are decane and water. The system like this: decane --- surfactant > --- water > --- surfactant --- decane My research is t

Re: [gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface

Very thank you for your suggestion and being so kind. I will write a new detailed subject and explain my purpose. On Sat, Jun 2, 2012 at 10:23 AM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote: > No, the point is that the equilibrium surface area is near zero in the > context of PBC a

[gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface

Dear Chris: Thank you for your help. Maybe I can try it as this. First set x and y fixed by setting compressibility = 0 4.5e-0.5 until the system reaching equilibrium and then release. If it sounds reasonable. I am trying to do it. Dear Hugh: I can't answer your question, but I can address the e

[gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface

Dear Gromacs users, I have do simulation of surfactant at oil/water interface for a long time. But I find it too difficult to get a reasonable interfacial tension. The key question is the pcoupltype. My system: Box size: 3.0 * 3.0 * 13 > Molecule Number: decane 230, water 2041 > pcoupltype = se