Re: [gmx-users] semi-permeable wall in gromacs

On 4/19/16 9:06 AM, gozde ergin wrote: Is refcoord_scaling the issue for also NVT simulation? No, it only applies when pressure coupling is applied. Because Roux and Luo did NVT after equilibrate the system in semiisoptropic NPT. The information you've provided (based on file names and

Re: [gmx-users] semi-permeable wall in gromacs

Is refcoord_scaling the issue for also NVT simulation? Because Roux and Luo did NVT after equilibrate the system in semiisoptropic NPT. > On 19 Apr 2016, at 14:06, Justin Lemkul wrote: > > > On 4/19/16 6:15 AM, gozde ergin wrote: >> This is my posre.itp file; >> >> [

Re: [gmx-users] semi-permeable wall in gromacs

On 4/19/16 6:15 AM, gozde ergin wrote: This is my posre.itp file; [ position_restraints ] ; i funct gr(nm) k 1 252.4 4184 2 252.4 4184 My box size is 4.8*4.8*9.6. In the reference.gro file z positions of all of the ions are set to 4.8 so I

Re: [gmx-users] semi-permeable wall in gromacs

This is my posre.itp file; [ position_restraints ] ; i funct gr(nm) k 1 252.4 4184 2 252.4 4184 My box size is 4.8*4.8*9.6. In the reference.gro file z positions of all of the ions are set to 4.8 so I have two walls at 4.8+2.4=7.2nm and

Re: [gmx-users] semi-permeable wall in gromacs

Yes it worked. I appreciated to your help Justin. Thanks a lot. > On 07 Apr 2016, at 21:37, Justin Lemkul wrote: > > > > On 4/7/16 12:57 PM, gozde ergin wrote: >> Hi Justin, >> >> I just want to ask how is the r(nm) in posre.itp working? >> >> I would like to put

Re: [gmx-users] semi-permeable wall in gromacs

On 4/7/16 12:57 PM, gozde ergin wrote: Hi Justin, I just want to ask how is the r(nm) in posre.itp working? I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the box. When I write 2.4 in the r(nm) property for [position_restraints] in posre.itp, it seems all of the

Re: [gmx-users] semi-permeable wall in gromacs

Hi Justin, I just want to ask how is the r(nm) in posre.itp working? I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the box. When I write 2.4 in the r(nm) property for [position_restraints] in posre.itp, it seems all of the molecules that I apply flat-bottom

Re: [gmx-users] semi-permeable wall in gromacs

On 3/21/16 1:29 PM, gozde ergin wrote: Ok this was a silly question. In g_energy command 5. one is flat-bottom posres force. Sorry. The output of g_energy is energy, not force. But the quantity is simple to calculate. If you have applied a flat-bottom restraint along z, then you just

Re: [gmx-users] semi-permeable wall in gromacs

Ok this was a silly question. In g_energy command 5. one is flat-bottom posres force. Sorry. > On 21 Mar 2016, at 17:26, gozde ergin wrote: > > Hey Justin, > > I am just wondering in order to estimate the osmotic pressure I need extract > the flat-bottom restraint

Re: [gmx-users] semi-permeable wall in gromacs

Hey Justin, I am just wondering in order to estimate the osmotic pressure I need extract the flat-bottom restraint force. (Force/Area = Pressure) Do you have any idea to how to extract this force? Thanks in advance > On 10 Mar 2016, at 15:58, Justin Lemkul wrote: > > > >

Re: [gmx-users] semi-permeable wall in gromacs

On 3/10/16 4:44 AM, gozde ergin wrote: Dear Justin, Thanks for your respond, I assume there is a way to apply this restraint on specific molecules. Because my system is mixed with organic and water and I would like to apply these forces on organic molecules not water? So apply

Re: [gmx-users] semi-permeable wall in gromacs

Dear Justin, Thanks for your respond, I assume there is a way to apply this restraint on specific molecules. Because my system is mixed with organic and water and I would like to apply these forces on organic molecules not water? > On 09 Mar 2016, at 18:30, Justin Lemkul

Re: [gmx-users] semi-permeable wall in gromacs

On 3/9/16 12:28 PM, gozde ergin wrote: Dear all, I would like to compute the osmotic pressure directly from all-atom MD simulations of concentrated aqueous solutions. The basic idea is to introduce “virtual” walls to represent the effect of ideal semipermeable membranes, separating a high

[gmx-users] semi-permeable wall in gromacs

Dear all, I would like to compute the osmotic pressure directly from all-atom MD simulations of concentrated aqueous solutions. The basic idea is to introduce “virtual” walls to represent the effect of ideal semipermeable membranes, separating a high concentration region from a pure water