Hello,
I have read somewhere in the list that I cannot do pressure coupling
without pbc.
What I essentially need is a box with impermeable walls, that get smaller
as the simulation proceeds.
I do anisotropic pressure coupling with two impermeable walls (in xy axis)
for another simulation, and it
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
Hello everyone. I want to know if can be applied pressure coupling only in
the z direction, allowing the edges x and y simulation box with fixed size.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.g
Hello All,
I have some doubts regarding the use of pressure coupling and
isothermal compressibility for a biphasic system (octane+water boxes
built over each other). I have two questions regarding that:
(1) Which pressure coupling (pcoupl) type would be suitable for this
type of system ?
(2) As
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
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 constant (ps), compressibility (1/bar) and referen
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
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
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? Isotropic 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
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
: 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
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
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 1 Warning: pressure scaling more than 1%,
Thank you Justin and Peter for your responses. I tried extending the time
on the npt equilibration. It helped but not much. My final pressure after
the MD run was about 1.15 bar compared to ref_p which was set to 1 bar.
Peter, I will try to analyze the potential error using RMSD and Drift.
Than
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
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 potential
energy, viewed it on VMD, again l
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
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 potential energy, viewed it on VMD, again
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
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?
thanks in advance,
Afsaneh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please
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
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
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 of pressure converge to 1
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
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
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
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 for temperature.) I run energy
Hi Gromacs Users,
Pressure coupling is not supposed to scale the coordinates of my frozen
group, yet it is. My frozen group is a crystal structure that does not have
any topology assigned to them: no bond, angle, dihedral constants etc.
specified. I find that a crystal structure gets compressed.
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
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
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
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
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
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 = 300
Pcoupl
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
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
Alright, sorry that I wasn't able to help. I'm confused by some
apparent contradictions in your posts and I'm not sure that I'm going
to be useful to you here.
Quoting
http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html: "No
matter how much minimization I do the volume of th
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
So your problem with the small water box was solved simply by adding more
minimization? I then suspect that all of your problems are simply related to a
bad starting structure -- and by the sound of it is really is very bad. Are you
sure that you don't have an angstrom / nm problem here?
Chris
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
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
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
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
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
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
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
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
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 for it just to be sure. Did you only give us a
partial mdp file?
Try adding this to your mdp file:
constraints = all-bonds
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
Hi Ilya,
If you did include the entire mdp file then you have a time step of 4
fs and no constraints (other than water). For a timestep of 2 fs, you
should constrain all-bonds (or some would say at least h-bonds) and
for 4 fs then you should also constrain angles involving hydrogens
(need
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
Hi
I am having some pressure coupling issues. I have a fairly large
protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
run NVE it conserves energy with appropriate parameter settings. If I run
NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
Rahman), the s
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 gromacs. In fact, I think that grompp/mdrun
should p
Hi all!
I am quite new to Gromacs and am wondering why I can´t see any box
fluctuations during a NPT run of protein + urea solvent in dodecahedron. In
the energy output file I can see that the Box-X,Y,Z values only fluctuate
<1%.
However the pressure average is reasonably close to the ref_p valu
Dear GMX-users,
I'm trying to do self-assembly of bilayer. I'm using coarse-grained model
(MARTINI), and there are 1280 CG lipids and 30110 CG waters. I followed
procedures of Marrink and de Vries's atomistic simulations of the bilayer
self-assembly. So, I simulated the randomly-positioned sy
Hello,
Would the following be a reasonable way to implement
anisotropic pressure coupling, for a 128 DPPC /3655
water bilayer with an aminoacid on it:
; Pressure coupling is on
Pcoupl = parrinello-rahman
pcoupltype = anisotropic
tau_p = 1.0 1.0 1.0 0 0 0
compressibility = 4.5e-5 4.5e-5 4.
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:
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: 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
Another suggestion is welcome.
Thanks in advance
Pragya
_
For example, a 3ns simulation using a tau_p of 0.5 I get
a surface tension of 30 dynes/cm and using a tau_p of 5.0 I get a surface
tension of 25 dynes/cm.
First thing that comes to mind is that your area per lipid is not at
equilibrium. Assuming that your bilayer normal lies in the Z
dimensi
Hello,
I am simulating a lipid bilayer system under a shear stress, in which I
am interested in looking at the surface tension. I have done a number of
simulations in an NPT ensemble using semiisotropic Berendsen pressure
coupling. For a system such as this, I am wondering what would be an o
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
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.
Hi,
I want to fix the pressure during the simulation so I use pressure
coupling. I set the reference potential to 1 (the unit is bar as the
manual says). Nevertheless, the log file shows much higher pressures
(can reach the order of 1e+03 and again it seems the unit is bar).
Moreover, it
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.
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. After about 1ps, t
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
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
suggestion of using a water s
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.
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 1.0e-30
ref_p = 1.0 1.0
[I'm not asking whether this will prod
70 matches
Mail list logo
