Re: [gmx-users] anisotropic pressure coupling

Shuangxing Dai wrote: Hi all: I was using Parrinello-Rahman for pressure coupling and here is the mdp file: ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps =

[gmx-users] anisotropic pressure coupling

Hi all: I was using Parrinello-Rahman for pressure coupling and here is the mdp file: ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; number of steps for

Re: [gmx-users] anisotropic pressure coupling

Shuangxing Dai wrote: Hi, all: I was trying to use pcoupl= Parrinello-Rahman, pcouptype=anisotropic to do pressure coupling for anisotropic material (like crystal). It seems that I need six components for compressibility (xx yy zz xy yz xz). How do I get these six components before I do a

[gmx-users] anisotropic pressure coupling

Hi, all: I was trying to use pcoupl= Parrinello-Rahman, pcouptype=anisotropic to do pressure coupling for anisotropic material (like crystal). It seems that I need six components for compressibility (xx yy zz xy yz xz). How do I get these six components before I do any MD simulation? Also, if th

RE: [gmx-users] Anisotropic pressure control

Behalf Of Matteus Lindgren Sent: Friday, 26 February 2010 8:24 PM To: gmx-users@gromacs.org Subject: [gmx-users] Anisotropic pressure control Dear experts, I am trying to run MD on a protein in water above a flat surface of TiO2 in a cubic box with pressure control. All the atoms of TiO2

[gmx-users] Anisotropic pressure control

Dear experts, I am trying to run MD on a protein in water above a flat surface of TiO2 in a cubic box with pressure control. All the atoms of TiO2 are frozen and I therefore think that anisotropic pressure control must be used. I tried allowing box fluctuations in the direction of the normal ve

Re: [gmx-users] anisotropic pressure coupling for temperature annealing

m: Q733 <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Wednesday, October 10, 2007 6:40:06 AM Subject: [gmx-users] anisotropic pressure coupling for temperature annealing Dear gmx-users, I used anisotropic p-coupling for lipid bilayers and annealed the system from 330K-300K at the rat

Re: [gmx-users] anisotropic pressure coupling for temperature annealing

Q733 wrote: > Dear gmx-users, I used anisotropic p-coupling for lipid bilayers and > annealed the system from 330K-300K at the ratio of 2 degree/ns.And the x > dimension and y dimension increased with time in the whole > procedure, but actually the area/lipid should decrease when tempreture > d

[gmx-users] anisotropic pressure coupling for temperature annealing

Dear gmx-users, I used anisotropic p-coupling for lipid bilayers and annealed the system from 330K-300K at the ratio of 2 degree/ns.And the x dimension and y dimension increased with time in the whole procedure, but actually the area/lipid should decrease when tempreture decreases. I think there

Re: [gmx-users] Anisotropic Pressure

Thanks Pedro, if I did not misunderstand you I should go for something like this: pcoupl = berendsen pcoupltype = surface-tension ref_p = 600 1.025 tau_p = 5.0 5.0 compressibility = 9.8e-5 4.53e-5 Is it correct? Hmmm... "Surface tension" is a tricky subject at the microscopic level. Besides

Re: [gmx-users] Anisotropic Pressure

Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote: > > > "The first ref_p value is the reference surface tension times the > number > of surfaces [bar nm]," > > I have a lipid bilayer membrane su I guess I should multiply by 2 the > surface tension value for which I do not h

Re: [gmx-users] Anisotropic Pressure

"The first ref_p value is the reference surface tension times the number of surfaces [bar nm]," I have a lipid bilayer membrane su I guess I should multiply by 2 the surface tension value for which I do not have any guess about its value. No. If you choose, as an example, 300 bar.nm (wich, b

Re: [gmx-users] Anisotropic Pressure

Berk Hess wrote: From: Matteo Guglielmi <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: GMX-LIST Subject: [gmx-users] Anisotropic Pressure Date: Fri, 15 Jun 2007 19:11:50 +0200 Hello Folks, Is there any difference b

RE: [gmx-users] Anisotropic Pressure

From: Matteo Guglielmi <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: GMX-LIST Subject: [gmx-users] Anisotropic Pressure Date: Fri, 15 Jun 2007 19:11:50 +0200 Hello Folks, Is there any difference between these two anisotropic pressure setup? ### 1st setup ###

Re: [gmx-users] Anisotropic Pressure

Matteo Guglielmi wrote: Hello Folks, Is there any difference between these two anisotropic pressure setup? have you tried? if so you know the result. if not, why not? ### 1st setup ### pcoupl = berendsen pcoupltype = anisotropic tau_p= 5.0

[gmx-users] Anisotropic Pressure

Hello Folks, Is there any difference between these two anisotropic pressure setup? ### 1st setup ### pcoupl = berendsen pcoupltype = anisotropic tau_p= 5.0 5.0 5.0 0.00.00.0 compressibility = 4.53e-5 4.53e-5 4.