Dear Mark,
Thank you very much for the quick reply to my post. According to your
suggestion, I check the table and reformat it with equal spacing between
entries. I also check the entries calculated from the analytical functions and
no wrong values are found. However, the same warnings are
Hi,
Last week another user reported very similar problems (also 164% deviations, I
think).
In that case it seemed that the user did an Angstrom to nm conversion in the
table file
on x without scaling f(x). Could this also be your issue?
Berk
From: xiaowu...@hotmail.com
To:
Dear Berk,
Unfortunately, this time it is angle (table_a0.xvg) that cause the problem.
The angles are taken in degrees. I think it is not due to the wrong unit.
Anyway, thanks very much for your reply.
Best wishes,
Chaofu Wu, Dr.
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject:
Hi,
But there could be a very similar issue there for the conversion from radians
to degrees.
The force has to be in units of kJ/mol/degree, not kJ/mol/radian.
Berk
From: xiaowu...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] a bit strange errors
Date: Fri, 16 Oct 2009
Dear Berk,
In fact, I calculated the potential and force from the analytical function of
angles in degrees, which is multicentred Gaussian-based potentials. So I think
it must be some other reasons that cause the issues. Anyway, thanks again for
your reply.
Best wishes,
Chaofu Wu, Dr.
For your information, the procedure is:
$ grompp ... (to generate minimize.tpr)
$ lamboot
$ l$ mdrun_mpi -np 4 -v -s minimize.tpr -o mod21_traj.trr -c mod21.gro
-e mod21_ener.edr
It worked nicely, exactly as the serial run mdrun -v -s minimize.tpr
No interference with installed openmpi,
Dear all,
is there any possibility to give the bond information out of GROMACS
files to VMD? Especially for coarse-grained models (using the MARTINI
FF) this would be a nice feature for visualization.
But in that case the distance analysis doesn't work, because we will
always have too high
Hi everyone,
in the last weeks I've been trying to run a simulation with Gromacs 4.0.5
and the force field ffamber99.
The protein is albumine (BSA, bovine serum albumine), so it's a very big one
(570+ residues).
The solvent is tip3p.
After an energy minimization run and a position restraint run,
Simone Cirri wrote:
snip
; Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1
tc-grps= protein sol NA+
ref_t = 300 300 300
Never couple solvent and ions
Hi,
I need to do an all atom simulation for dppc bilayer . You are right
the
dppc molecule file that i have has PALM and PCGL residues.
Well, I don't know where you got the dppc molecule from, I thought you
said you didn't have any DPPC structure with hydrogens? Anyway, I'll
send you the
Simone Cirri wrote:
Justin A. Lemkul wrote:
; Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+
ref_t = 300 300 300
Never couple solvent and ions separately. Surely
Hi Simone,
The temperature coupling might be a cause for an error like that to
occur. Try to understand that coupling ions separately may cause large
fluctuations in there velocities and hence cause sudden large
displacements that may put an ion on top of a solvent molecule that
can't be settled
Hi
I am new to Gromacs and going through some tutorials. I am working on
lipid-protein tutorial given by Justin Lemkul and I am stuck with the
very first step. When I execute pdb2gmx to generate .top file and .pdb
without hydrogen,
pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh
Dear Gromacs users,
I am doing protein in lipid-bilayer simulation and i am following the
procedure as per justin tutorial. I am able to insert the protein in
lipid bilayer and minimize the system as per Inflategro
procedure,during the total procedure the system was minimized in every
step.Then,
Dear Gromacs users,
I am doing protein in lipid-bilayer simulation and i am following the
procedure as per justin tutorial. I am able to insert the protein in
lipid bilayer and minimize the system as per Inflategro
procedure,during the total procedure the system was minimized in every
step.Then,
seunghwan lee wrote:
Hi
I am new to Gromacs and going through some tutorials. I am working on
lipid-protein tutorial given by Justin Lemkul and I am stuck with the
very first step. When I execute pdb2gmx to generate .top file and .pdb
without hydrogen,
pdb2gmx -f KALP-15_princ.pdb -o
ram bio wrote:
Dear Gromacs users,
I am doing protein in lipid-bilayer simulation and i am following the
procedure as per justin tutorial. I am able to insert the protein in
lipid bilayer and minimize the system as per Inflategro
procedure,during the total procedure the system was minimized
Dear Justin,
Thanks and I tried your suggestion, that is minimizing the system
without restraints and increasing the Fmax to 1000, the mdp file used
is as follows:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
Hi Justin,
Thank you for your answer. It made me to think again and I found the
source of the problem (silly mistake). Thanks again!
Seunghwan Lee
--- On Fri, 10/16/09, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Lipid-protein
Hello,
In a simulation, how is it possible to extract the profiles e.g.
potential as a function of z (coordinate axis of box)?
Payman
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Hi,
This of course depends very much on all your settings.
Up to now I have found that a 3:1 ratio is optimal for rectangular boxes,
whereas 2:1 is optimal for rhombic dodecahedra.
64 cores was the limit for the benchmark system on that hardware,
so I had to increase the number of PME beyond the
Paymon Pirzadeh wrote:
Hello,
In a simulation, how is it possible to extract the profiles e.g.
potential as a function of z (coordinate axis of box)?
g_potential can do this for electrostatic potential, but I don't know about
anything else. I don't think it is a trivial question to
Well, the main purpose is to average the energy or any desired property
along any desired coordinate axis. simple binning of the box will do the
job, but I was wondering if this can be done in general with gromacs
post simulation tools.
Payman
On Fri, 2009-10-16 at 16:05 -0400, Justin A. Lemkul
Hello fellow GROMACS users!
I've been having a heck of a time with the reformatting of a DNA molecule
into a GROMACS-compatible format. I know that residues (bases) must be
renamed to DTHR, etc., though it would be endlessly helpful if someone could
please send me an example pdb or gmx file I
David Crosby wrote:
Hello fellow GROMACS users!
I've been having a heck of a time with the reformatting of a DNA molecule
into a GROMACS-compatible format. I know that residues (bases) must be
renamed to DTHR, etc., though it would be endlessly helpful if someone could
please send me an
Dear,
I want to do stochastic simulations in the framework of Langevin dynamics
using Gromacs with the reduced units. The questions are:
1. How to turn on the reduced units? Is there any parameters for setting?
2. If I use the reduced temperature of 1, should the ref_t in the .mdp file
be the
Paymon Pirzadeh wrote:
Well, the main purpose is to average the energy or any desired property
along any desired coordinate axis. simple binning of the box will do the
job, but I was wondering if this can be done in general with gromacs
post simulation tools.
No, there is no general way to do
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