Dear users,
I would be most thankful for any comment or advice on the following
problems:
1. I'm running GROMACS 4.04 with amber V_4.0. /amber99sb forcefield.
While executing the pdb2gmx command as: pdb2gmx -f 1bgq.pdb -water tip3p
-his
the -his option does not work regardless of the choice
Hi,
I am having trouble with running gromacs with a large system. I am trying to
use several processors for the md. The error is a memory allocation error
and it might be due to low RAM or large no of particles. I want to know the
detailed memory usage of mdrun ie say for N atoms how much memory
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
Dear all,
I have some doubt regarding energy minimization and the use of
constraint algorithms (such as LINCS) that may come from my
inexperience in GROMACS and molecular dynamics in general.
In a Berk Hess talk given at the GROMACS workshop 2007 it is stated:
Hi,
It seems there is a bug in grompp, which subtracts degrees of freedom for
constraints in water also for frozen water molecules.
I guess the md.log file reports zero degrees of freedom for your t-coupl group.
You can circumvent this issue by putting all your frozen atoms in a separate
pa...@ncbs.res.in wrote:
Dear All,
I'm a new comer to gromacs. I need to perform molecular dynamics
simulation of my protein within the POPC membrane. I have downloaded the
128a popc lipid from Prof.Tieleman's group along with the required
popc.itp. My protein of interest is 458 residues.
Arik Cohen wrote:
Dear users,
I would be most thankful for any comment or advice on the following
problems:
1. I'm running GROMACS 4.04 with amber V_4.0. /amber99sb forcefield.
While executing the pdb2gmx command as: pdb2gmx -f 1bgq.pdb -water tip3p
-his
the -his option does not work
Hi,
I've been trying to go through the 'Introduction to Molecular Dynamics
Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of
the tutorials listed on the GROMACS website.
I've got to the stage where I am performing energy minimisation on my
solvated protein but when I
Hi,
This all depends on what you want to achieve.
In most cases energy minimization is used to remove atomic overlap from
a bad starting structure or from slightly overlapping solvent atoms.
If you run your MD with constraints, you probably also want constraints
during the (last) minimization
You will need an up to date version of MPI or PVM. Set USE_MPI or USE_PVM to
yes in your Makefile.$GMXCPU and type:
cd $GMXHOME/src
in which file should i type this? I can find makefile.in and makefile.am in the
distribution directory where I unpack GROMACs and in the src directory. Which
of
Hi Anna,
You should mention the version of Gromacs you're using. One of the
versions did not write the box correctly to pdb files, which I think
happened in your case. If you take as the solvation step
genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro
instead of writing
Dear Berk,
Thanks for your response, As you mentioned i have separated t-coupling group
for frozen and non-frozen groups, still the result is same.
Herewith i am giving my md.mdp file, Can you suggest me if i am missing any
options in my md.mdp file?
Thanks again
Srinivas.
md.mdp file
Hi,
Then I have no clue what might be wrong.
Have you check nrdf in the log file?
Berk
Date: Fri, 26 Feb 2010 09:54:22 -0500
Subject: Re: [gmx-users] problem with the size of freeze groups
From: jampa...@gmail.com
To: gmx-users@gromacs.org
Dear Berk,
Thanks for your response, As you mentioned
See here:
http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions
(You don't need to change any files - instead you call ./configure
--enable-mpi)
On Fri, Feb 26, 2010 at 8:49 AM, Andrew Voronkov drugdes...@yandex.ruwrote:
You will need an up to date version
HI
Thanks, My log file shows me nrdf: 0
###
grpopts:
nrdf: 0
ref_t:0
tau_t: 0
###
Thanks
Srinivas.
On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote:
Hi,
Then I have no clue what might be wrong.
Ah, but that does not correspond to the mdp options tou mailed.
Here there is only one group with 0 degrees of freedom and reference
temperature 0.
Berk
Date: Fri, 26 Feb 2010 10:50:13 -0500
Subject: Re: [gmx-users] problem with the size of freeze groups
From: jampa...@gmail.com
To:
Hi Berk,
I am extremely sorry, here is the correct log file
grpopts:
nrdf: 0 0
ref_t: 300 0
tau_t: 0.1 0.1
Thanks
Srinivas.
On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote:
Hi all,
Please, can someone let me know if the choice of the value of rlist, rvdw
and rcoulomb is related to or depends in someway to the distance between
atoms on a lennard-jones potential plot?
I appreciate your answers.
Lum
--
gmx-users mailing listgmx-users@gromacs.org
Dear Berk,
It looks to me some thing is wrong when i change the radius from 35 to 25,
herewith i am giving grpopts for both systems
+
grpopts: (system with 35 A)
nrdf: 33141.4 0
ref_t: 300 0
tau_t: 0.1 0.1
That is what I suspected, by I don't know why this is.
Are you really sure you made a temperature coupling group
that is exactly the freeze group?
This first mdp file you mailed had a different group names for the freeze group
and the tcoupl groups.
Berk
Date: Fri, 26 Feb 2010 11:53:49 -0500
Dear Berk,
They are same, freeze and Tmp2 are exactly the same groups. I just put them
like that for my convenience, just to avoid confusion in my second email i
made it uniform.
Thanks
Srinivas.
On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess g...@hotmail.com wrote:
That is what I suspected, by
Hi,
Which version of Gromacs are you using?
I can't see any issues in the 4.0 code, but some older version might have
problems.
Berk
Date: Fri, 26 Feb 2010 12:05:56 -0500
Subject: Re: [gmx-users] problem with the size of freeze groups
From: jampa...@gmail.com
To: gmx-users@gromacs.org
Dear
Dear Justin,
Many thanks for your comprehensive mail. I will try to do it and let you
know if i come across any problem..(Definetely i may bug u again :))
Thank you so much.
Best regards
Padhu
pa...@ncbs.res.in wrote:
Dear All,
I'm a new comer to gromacs. I need to perform molecular dynamics
Dear Berk,
I am using VERSION 4.0.5. As you said if there is no problem i should get it
correctly, i don't know where it is going wrong. I have written a small
script in tcl to use in vmd to get my selections. i will check the script
and the selection again. I will let you know my results again.
Hi Lum,
These values have to be chosen very icarefully.
Many artifacts can show up due to poorly chosen cutoff. I would suggest to
get the parameters from a reproducible publication or something.
amit
On Fri, Feb 26, 2010 at 8:49 AM, Lum Nforbi lumngwe...@gmail.com wrote:
Hi all,
Please,
Thanks a lot for the quick response
Arik
On 2/26/2010 3:54 AM, Justin A. Lemkul wrote:
Arik Cohen wrote:
Dear users,
I would be most thankful for any comment or advice on the following
problems:
1. I'm running GROMACS 4.04 with amber V_4.0. /amber99sb forcefield.
While executing the
Dear Berk,
I have checked my inputs and tcl scripts that i have used for the selection,
i could see that my selection doesn't have any problem.
I submitted it again still i am getting the same log file with nrdf 0 for
non-freezing group. Please let me know if you want see any of my input
files,
- Original Message -
From: Lum Nforbi lumngwe...@gmail.com
Date: Saturday, February 27, 2010 3:51
Subject: [gmx-users] Choice of value of rlist, rvdw and rcoulomb
To: gmx-users@gromacs.org
Hi all,
Please, can someone let me know if the choice of the value of rlist, rvdw
and
Hello,
This is the third time I am sending this e-mail, and I am not sure why it
does not show up on the list
I have a simulation from which I have the .edr, .xtc and .trr files. I want
to color my particles based on rmsd, potential energy, Sg (tetrahedral
parameter) or any other parameters
- Original Message -
From: Amit Choubey kgp.a...@gmail.com
Date: Friday, February 26, 2010 20:05
Subject: [gmx-users] gromacs memory usage
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi,
I am having trouble with running gromacs with a large system. I am trying to
use
Your message certainly has appeared, and received replies:
http://lists.gromacs.org/pipermail/gmx-users/2010-February/049002.html
You can always check the thread to see if it's hit the list.
-Justin
Payman Pirzadeh wrote:
Hello,
This is the third time I am sending this e-mail, and I am not
- Original Message -
From: Payman Pirzadeh ppirz...@ucalgary.ca
Date: Saturday, February 27, 2010 9:55
Subject: [gmx-users] extracting individual particles properties
To: gmx-users@gromacs.org
This is the third time I am sending this e-mail, and I am
not sure why it does not show up on
Hi Mark,
We have few nodes with 64 GB memory and many other with 16 GB of memory. I
am attempting a simulation of around 100 M atoms.
I did find some document which says one need (50bytes)*NATOMS on master
node, also one needs
(100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes.
- Original Message -
From: Amit Choubey kgp.a...@gmail.com
Date: Saturday, February 27, 2010 10:17
Subject: Re: [gmx-users] gromacs memory usage
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi Mark,
We have few nodes with 64 GB memory and many other with 16 GB of memory.
Hi gromacs users:
As you know autocorrelation function C(t)
C(t) = f(0).f(t)
't' value can start from 0 but, i would like to know what value does
gromacs use, more specifically for g_hbond.
Can anyone help me? Thank you.
Rama
--
gmx-users
On 2010-02-27 03.27, Ramachandran G wrote:
Hi gromacs users:
As you know autocorrelation function C(t)
C(t) = f(0).f(t)
't' value can start from 0 but, i would like to know what value does
gromacs use, more specifically for g_hbond.
Can anyone help
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