Re: [gmx-users] Pressure coupling

Probably. See manual 7.3.15. Semiisotropic with some zero compressibilities is probably what you want. Mark On Sun, Jun 2, 2013 at 9:33 PM, Marcelo Vanean wrote: > Hello everyone. I want to know if can be applied pressure coupling only in > the z direction, allowing the edges x and y simulatio

Re: [gmx-users] Pressure coupling doubt

On 29/03/2012 5:38 PM, bipin singh wrote: Hello, I have two doubts regarding pressure coupling in Gromacs: 1) When I use pcoupl=no the mdp.out shows the following ; Pressure coupling pcoupl = no Pcoupltype = Isotropic nstpcouple = -1 ; Time consta

Re: [gmx-users] Pressure coupling and membrane-type simulations

On 2012-02-21 03:41:07PM -0500, Justin A. Lemkul wrote: > > > Andrew DeYoung wrote: > > Hi, > > > > I am interested in doing a membrane-type simulation, in which I have > > all-atom membrane "walls" parallel to xy plane, at z = -z_0 and z = +z_0 > > (where z_0 is a constant). I would like to ru

Re: [gmx-users] Pressure coupling and membrane-type simulations

Andrew DeYoung wrote: Hi, I am interested in doing a membrane-type simulation, in which I have all-atom membrane "walls" parallel to xy plane, at z = -z_0 and z = +z_0 (where z_0 is a constant). I would like to run an NPT simulation at 1 atm. What type of pressure coupling should I use? Is

Re: [gmx-users] pressure coupling

From: Mark Abraham To: Discussion list for GROMACS users Sent: Saturday, December 17, 2011 10:22 AM Subject: Re: [gmx-users] pressure coupling On 17/12/2011 5:40 PM, mohammad agha wrote: Thank you very much. >Excuse me, I did another thing, may I know is it ri

Re: [gmx-users] pressure coupling

st Regards Sara *From:* Mark Abraham *To:* Discussion list for GROMACS users *Sent:* Saturday, December 17, 2011 9:31 AM *Subject:* Re: [gmx-users] pressure coupling On 17/12/2011 4:58 PM, mohammad agha wrote: Dear GROMACS Users I have a warn

Re: [gmx-users] pressure coupling

: Saturday, December 17, 2011 9:31 AM Subject: Re: [gmx-users] pressure coupling On 17/12/2011 4:58 PM, mohammad agha wrote: Dear GROMACS Users > > >I have a warning after doing pr.mdp as followed, I read errors in GROMACS site >and checked mailing list, but my warning is only step1 an

Re: [gmx-users] pressure coupling

On 17/12/2011 4:58 PM, mohammad agha wrote: Dear GROMACS Users I have a warning after doing pr.mdp as followed, I read errors in GROMACS site and checked mailing list, but my warning is only step1 and after that equilibration is run normally till end. 500 steps, 15.0 ps. step 0 Step

Re: [gmx-users] Pressure coupling problem

So your density graph looks stabilized? I also tend to look for changes in box x, y, z as well since the scale of their changes is easier to track. Sometimes it helps to look at the error vs. rmsd vs total drift statistics as well for such parameters that are easier to track - again if density sh

Re: [gmx-users] Pressure coupling problem

Fabian Casteblanco wrote: Hi, I'm still in my first few months of using Gromacs. I started by creating an *.itp and *.top file for /Ethanol/ using CHARMM force field parameters. I made the molecule and it looked fine, put 1000 molecules in a box, energy minimized it to a negative potenti

Re: [gmx-users] pressure coupling not enough values (I need 2)

afsaneh maleki wrote: Hi, grompp show the error as below: ERROR: pressure coupling not enough values (I need 2) I used ref_p =1. In file.mdp How to solve this problem? Without seeing the rest of your pressure coupling settings, I can only assume that you're using semi-isotr

Re: [gmx-users] Pressure coupling

On 2010-07-15 16.01, Justin A. Lemkul wrote: Sai Pooja wrote: Hi, I am aware there have been many threads on this topic and I have looked at some of them. I would still like to make this query. I am running an npt equilibration run for a solvated protein using Charmm27-Tip3p (nocmap). I ran t

Re: [gmx-users] Pressure coupling

Sai Pooja wrote: Hi, I am aware there have been many threads on this topic and I have looked at some of them. I would still like to make this query. I am running an npt equilibration run for a solvated protein using Charmm27-Tip3p (nocmap). I ran the simulation for 1ns. The average values o

Re: [gmx-users] pressure coupling

subject to large fluctuations (due to its size). -Justin Message: 1 Date: Mon, 05 Jul 2010 10:39:30 -0400 From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> Subject: Re: [gmx-users] pressure coupling To: Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>> M

Re: [gmx-users] pressure coupling

do not know the criteria of Gromacs. Or maybe my procedure is wrong? Message: 1 Date: Mon, 05 Jul 2010 10:39:30 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] pressure coupling To: Discussion list for GROMACS users Message-ID: <4c31eea2.7070...@vt.edu> Content-Type: tex

Re: [gmx-users] pressure coupling

Shuangxing Dai wrote: Hi, all, I am trying to do anisotropic coupling using Parrinello-Rahman. I want to reach the equilibrium state at 1000K, 0.1MPa( 1 bar). However, I find that the fluctuation is so large ( p=80.22 bar, T=1007.23 K, fluctuation is 626 bar for pressure and 11.21 K fo

Re: [gmx-users] Pressure coupling and cut-off

Yanmei Song wrote: Dear Justin: Thank you for your suggestions. using shift for vdwtype helps a lot. Can I ask you another question? The density of my system is about 8% larger than the experimental value. Do you have any suggestions on how to reduce the density of the system. Or once the f

Re: [gmx-users] Pressure coupling and cut-off

Dear Justin: Thank you for your suggestions. using shift for vdwtype helps a lot. Can I ask you another question? The density of my system is about 8% larger than the experimental value. Do you have any suggestions on how to reduce the density of the system. Or once the force field and all the pa

Re: [gmx-users] Pressure coupling and cut-off

Yanmei Song wrote: Dear Justin: Thanks for your response. Here is the complete my .mdp file: title = pdm cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 250 ; total 10n

Re: [gmx-users] Pressure coupling and cut-off

Dear Justin: Thanks for your response. Here is the complete my .mdp file: title = pdm cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 250 ; total 10ns. nstcomm

Re: [gmx-users] Pressure coupling and cut-off

Yanmei Song wrote: Dear All: I have question about the pressure coupling. I have done a 10ns simulation with 19800 atoms for 120 large molecules using the following pressure coupling. Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t

Re: [gmx-users] Pressure Coupling Problem

bject: Re: [gmx-users] Pressure Coupling Problem I finally figured it out. I went through every parameter step by step and it turns our I had epsilon-r set to 80. Not sure why I had that. Wish gromacs would have given me a warning (hint hint). That explains why my P.E. was 10^-5 instead of

Re: [gmx-users] Pressure Coupling Problem

I finally figured it out. I went through every parameter step by step and it turns our I had epsilon-r set to 80. Not sure why I had that. Wish gromacs would have given me a warning (hint hint). That explains why my P.E. was 10^-5 instead of 10^-6. Thanks everyone for trying!!!. Sometime the most o

Re: [gmx-users] Pressure Coupling Problem

Nope not an A/nm problem. As a simple test I take spc.gro from share/top. I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o water_center. I then solvate with genbox, minimize and run using the mdp file I provided earlier. No matter how much minimization I do the volume of the

Re: [gmx-users] Pressure Coupling Problem

On Thu, Apr 9, 2009 at 6:36 AM, Justin A. Lemkul wrote: > > > Joe Joe wrote: > >> So I got my small water box (800 waters) to behave stably with pressure >> coupling after more minimization but I still can't get my large system to >> work with pressure coupling. I tried minimizing but I can never

Re: [gmx-users] Pressure Coupling Problem

Joe Joe wrote: So I got my small water box (800 waters) to behave stably with pressure coupling after more minimization but I still can't get my large system to work with pressure coupling. I tried minimizing but I can never get the Fmax to be less 10^2, which is pretty normal for protein/wat

Re: [gmx-users] Pressure Coupling Problem

So I got my small water box (800 waters) to behave stably with pressure coupling after more minimization but I still can't get my large system to work with pressure coupling. I tried minimizing but I can never get the Fmax to be less 10^2, which is pretty normal for protein/water simulations of lar

Re: [gmx-users] Pressure Coupling Problem

On Wed, Apr 8, 2009 at 11:31 AM, Roland Schulz wrote: > > > On Wed, Apr 8, 2009 at 7:53 AM, Joe Joe wrote: > >> HI Chris, >> >> On Tue, Apr 7, 2009 at 9:31 PM, wrote: >> >>> Hi Ilya, >>> >>> First thing that comes to mind is that it is strange to couple a >>> coulombic switching function with P

Re: [gmx-users] Pressure Coupling Problem

I tried .1, and 10 ps tau_p values. I guess I can try smaller values. On Wed, Apr 8, 2009 at 10:44 AM, Justin A. Lemkul wrote: > > > Joe Joe wrote: > >> Hi Chris, >> >> When I create the topology for the 4fs timestep I use pdb2gmx -vsite h. I >> set up the correct constraints. I've tested it a

Re: [gmx-users] Pressure Coupling Problem

Yeah I only gave a partial. Tried to remove the QM params. I do use constraints = all-bonds. On Wed, Apr 8, 2009 at 9:18 AM, wrote: > You say "I run all he sims with constraints=all-bonds", but I don't see > that in the mdp options that you provided. I even put your text in a file > and grepped

Re: [gmx-users] Pressure Coupling Problem

On Wed, Apr 8, 2009 at 7:53 AM, Joe Joe wrote: > HI Chris, > > On Tue, Apr 7, 2009 at 9:31 PM, wrote: > >> Hi Ilya, >> >> First thing that comes to mind is that it is strange to couple a coulombic >> switching function with PME. While this could possibly be done correctly, I >> doubt that it is

Re: [gmx-users] Pressure Coupling Problem

Joe Joe wrote: Hi Chris, When I create the topology for the 4fs timestep I use pdb2gmx -vsite h. I set up the correct constraints. I've tested it and it conserves energy in NVE. I run all he sims with constraints=all-bonds. I am now running a single water box (800 water molecules) with 1s t

Re: [gmx-users] Pressure Coupling Problem

Hi Chris, When I create the topology for the 4fs timestep I use pdb2gmx -vsite h. I set up the correct constraints. I've tested it and it conserves energy in NVE. I run all he sims with constraints=all-bonds. I am now running a single water box (800 water molecules) with 1s time steps and the volum

Re: [gmx-users] Pressure Coupling Problem

HI Chris, On Tue, Apr 7, 2009 at 9:31 PM, wrote: > Hi Ilya, > > First thing that comes to mind is that it is strange to couple a coulombic > switching function with PME. While this could possibly be done correctly, I > doubt that it is in fact done in the way that you expect (i.e. correctly) in

Re: [gmx-users] pressure coupling for bilayers

semiisotropic is more indicated for bilayers. pragya chohan <[EMAIL PROTECTED]> wrote: hi i want to rum a NPT ensemble on my bilayer+protein system. What is the best pcoupletype to use. I have seen some posts on gmx user group advising anisotriopic type with tau_p 5.0 ps cpmpressibility:

Re: [gmx-users] Pressure Coupling

Thank you very much for the reply, and I'll try to better search the board first :) Cheers, George Dallas B. Warren wrote: Issue like this has been discussed previously, try searching the emailing list for a solution first before posting. Means you get your answer faster :-) Pressure is a ma

RE: [gmx-users] Pressure Coupling

Issue like this has been discussed previously, try searching the emailing list for a solution first before posting. Means you get your answer faster :-) Pressure is a macroscopic property that is being monitored and adjusted on a microscopic scale. A variation of that order is entirely normal.

Re: [gmx-users] Pressure coupling question

toma0052 wrote: Hello, I am simulating a lipid bilayer system, and am having some trouble understanding the pressure output. When I run a simulation, even when I do not add any perturbations or fix any atoms, the pressure oscillations are quite large. The temperature coupling seems fine.

Re: [gmx-users] Pressure coupling appears to produce errors on the P655+ aix 5.2

Arthur Roberts wrote: Hi, All, I would like to thank Carsten Kutzner, Erik Lindahl, and David van der Spoel for their advise with my previous problem with not getting any data with mdrun. It turned out to be due to the fourier spacing and the PME order. In addition, David van der Spoel's sugge

Re: [gmx-users] Pressure Coupling for Lipid Bilayers

Hi, On May 11, 2006, at 6:05 PM, Arneh Babakhani wrote: Hello, Would the following be a reasonable way to implement semiisotropic pressure coupling, for a 128 DMPC membrane: ; Pressure coupling is on Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 1.