Dear Gromacs user,
I am trying to simulate a protein (nmr structure).I have successfully done
energy minimisation step.Also I have equilibrated the system a 298 k (which
is achieved from 100 ps run) .Now,I am trying to equilibrate the system at
1 bar pressure.After a run of 100 ps ,I am getting
Hi,
Parrinello-Rahman coupling usually allows wide fluctuations in the
pressure. I would suggest to take Berendsen algorithm for equilibrating
your system, and then extend the simulation with PR if you need to.
Bests,
baptiste
2013/10/14 Preeti Choudhary preetichoudhary18111...@gmail.com
The barostat tries to equilibrate the system at the desired pressure, there
will be fluctuations and these fluctuations are little higher for
Parrinello-rahman if started far away from equilibrium value. I would
suggest to start from berendsen and then extend it to P-R. Also, you should
run little
http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling and
http://www.gromacs.org/Documentation/Terminology/Pressure are useful here.
Mark
On Mon, Oct 14, 2013 at 4:32 PM, srinathchowdary
srinathchowd...@gmail.comwrote:
The barostat tries to equilibrate the system at the desired
HI all..
I am doing npt of protein-ligand complex. Now in that error is comingPressure
scaling more than 1%. How can I overcome this problem?
--
[image: images[12]]
“Many Smiles Begin Because Of Another Smile . . . .
Regards,
Rashi
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gmx-users mailing list
On 16/05/2011 4:26 PM, rashi parihar wrote:
HI all..
I am doing npt of protein-ligand complex. Now in that error is
comingPressure scaling more than 1%. How can I overcome this problem?
IIRC that's a warning, not an error. You simulation system was far
enough from its equilibrium size that
In God We Trust
Hello everyone
We have a problem for equilibrate the system with a protein within
POPE. we have searched mailing list , we dident any good note. We have used
pope.pdb from Dr. Tielemans website. We have inserted our protein into pope
and minimized it and equilibrated it with
Mahnam wrote:
In God We Trust
Hello everyone
We have a problem for equilibrate the system with a protein within
POPE. we have searched mailing list , we dident any good note. We have
used pope.pdb from Dr. Tielemans website. We have inserted our protein
into pope and minimized it and
Dear all,
I've tried to simulate a membrane system with POPC and protein following
Justin's tutorial. The system was minimized with 2 stages. First using
restraint on everything accept water for 1 SD steps:-
Steepest Descents converged to Fmax 1000 in 1785 steps
Potential Energy =
Bing Bing wrote:
Dear all,
I've tried to simulate a membrane system with POPC and protein following
Justin's tutorial. The system was minimized with 2 stages. First using
restraint on everything accept water for 1 SD steps:-
Steepest Descents converged to Fmax 1000 in 1785 steps
Potential
Hi,
have you checked if there is no water inside the membrane after the
use of genbox?
On Dec 16, 2007 1:35 PM, Mark Abraham [EMAIL PROTECTED] wrote:
pragya chohan wrote:
i started with the lipid coordinates from peter tieleman and removed the
water. then i added water by genbox.
I did
ya i removed every water molecule that entered the bilayers. after pr should i
do nvt before doing npt? i am doing position restrain also under npt. Date:
Mon, 17 Dec 2007 11:27:01 +0200 From: [EMAIL PROTECTED] To:
gmx-users@gromacs.org Subject: Re: [gmx-users] problem with npt Hi, have
you
pragya chohan wrote:
i started with the lipid coordinates from peter tieleman and removed the
water. then i added water by genbox.
I did energy minimization followed by position restrain, which I removed
gradually. all of it was done under npt. I carried out npt for 250
ps. During the next
In our experience the leaflets of a bilayer have a tendency to
separate if the cutoff on the van der Waals force is too short. We
always use 18-20 angstroms for that.
At 05:35 AM 12/16/2007, you wrote:
pragya chohan wrote:
i started with the lipid coordinates from peter tieleman and
removed
look quite strange
under NVT, but after a nanosecond or two or NPT they even out and behave
normally.
-Justin
Date: Sat, 15 Dec 2007 06:03:27 +1100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] problem with npt
pragya
the bilayers separated and deformed. Date: Sat, 15
Dec 2007 09:53:06 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org
Subject: RE: [gmx-users] problem with npt Quoting pragya chohan [EMAIL
PROTECTED]: I wrote yes to generate velocity. Can that be a reason
for the problem? Since I am doing
10
compressibility = 4.5e-5 4.5e-5
; Energy monitoring
energygrps = POPC SOL
Can anyone help?
Date: Wed, 5 Dec 2007 11:27:40 +1100
Subject: Re: [gmx-users] problem with npt
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
pragya chohan wrote:
thanks for your help.
My system ran fine for 250 ps but later the bilayer deformed very much.
What was your system preparation protocol - i.e. minimization and
equilibration? See
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
Mark
Dear users
I was tyring to run an npt simulation of membrane. My mdp is:
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5 ; total 100 ps.
nstcomm = 1
nstxout = 250
nstenergy = 100
nstlist = 10
ns_type = grid
pbc = xyz
coulombtype = PME
vdwtype = cut-off
; Berendsen
On Tue, 4 Dec 2007 05:56:22 +
pragya chohan [EMAIL PROTECTED] wrote:
Dear users
I was tyring to run an npt simulation of membrane. My mdp is:
The changes you observe are not dramatic. Why this seems a problem
to you?
I could not find the actual values of cut-off for vdw interactions.
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