On 2010-10-13 01.54, chris.ne...@utoronto.ca wrote:
I have 28,000 .xtc files, each having a single frame and each 150K. If I
run du -hs on the directory containing these .xtcs, I get 4.4 GB.
Nevertheless, when I run trjcat -f *.xtc -o ../tot.xtc , my memory
consumption goes over 11 GB and then I
Chris,
one quick look at the code suggest that the reason is that the memory isn't
freed correctly. read_first_frame is allocating the memory for one frame but
in most cases it isn't freed. Thus you only see this error with many small
files.
Since it is open source the best way to get it fixed, i
Thanks Justin. I got it now.
-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Wednesday, October 13, 2010 12:07 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Equilibration of POPC - Lipid
On 13/10/2010 5:01 PM, Mark Abraham wrote:
On 13/10/2010 4:55 PM, Sathish wrote:
Dear Mark,
Thanks for your reply. In my server gromacs installed at
"local/gromacs". I have checked out point 8 as you mentioned.
It was working with this "source /local/gromacs/bin/GMXRC" command.
That's
On 13/10/2010 4:55 PM, Sathish wrote:
Dear Mark,
Thanks for your reply. In my server gromacs installed at
"local/gromacs". I have checked out point 8 as you mentioned.
It was working with this "source /local/gromacs/bin/GMXRC" command.
That's all you need to do, in every shell from whi
Dear Mark,
Thanks for your reply. In my server gromacs installed at
"local/gromacs". I have checked out point 8 as you mentioned.
It was working with this "source /local/gromacs/bin/GMXRC" command.
and also tried , entered "local/gromacs/bin" path and calling to GMXRC but
it shows error
[r.
Thank you for the insight Mark.
To get it on the record, this is fairly annoying for trjcat (not
trjconv). If anyone else has run into this, then please do post
because a memory efficient cat mechanism will only be coded if there
is sufficient interest.
But again, thanks for your good ans
- Original Message -
From: Sathish
Date: Wednesday, October 13, 2010 14:31
Subject: [gmx-users] Gromacs installation problem @ RHEL5.5 server
To: gmx-users@gromacs.org
> Dear all,
> I have compiled and installed gromacs 4.5.1 on RHEL5.5 server. I have also
> installed openmpi-1.2.8, ff
Dear all,
I have compiled and installed gromacs 4.5.1 on RHEL5.5 server. I have also
installed openmpi-1.2.8, fftw-3.2.2 and gsl-1.11. After gromacs 4.5.1
installation did make tests and make links. Finally got message "GROMACS is
installed under /root/software" and "binary executable installed
/u
- Original Message -
From: chris.ne...@utoronto.ca
Date: Wednesday, October 13, 2010 10:55
Subject: [gmx-users] why does trjcat take so much memory?
To: gmx-users@gromacs.org
> I have 28,000 .xtc files, each having a single frame and each
> 150K. If I run du -hs on the directory contain
> >GROMACS performance is dependent on
> >a) non-bonded kernels (which are coded in assembler for the
> large majority of platforms for which icc exists, and so
> compiler version is largely irrelevant)
>
> I use mostly tabulated functions for the model I'm developing...
So does regular PME, an
I have 28,000 .xtc files, each having a single frame and each 150K. If
I run du -hs on the directory containing these .xtcs, I get 4.4 GB.
Nevertheless, when I run trjcat -f *.xtc -o ../tot.xtc , my memory
consumption goes over 11 GB and then I run out of available memory.
Sure, I could fin
Sanku M wrote:
Hi Tom,
I hoped that I could self-assemble the bilayer around the peptide.
But, the problem is how to do that. I am aware of the tutorial in the
Martini website. But, in that case, they use genbox -ci option to insert
certain lipid molecules in an EMPTY box. But, I guess gen
Hi Tom,
I hoped that I could self-assemble the bilayer around the peptide. But, the
problem is how to do that. I am aware of the tutorial in the Martini website.
But, in that case, they use genbox -ci option to insert certain lipid molecules
in an EMPTY box. But, I guess genbox -ci option will
Hi,
I am studying Potential of mean force(PMF) of association of two peptides. I
want to decompose the PMF into energy(enthalpy) and entropic terms. But, I
have
some queries on how to extract those contributions .
I found, in literature, generally, people try to get the energy(enthalpy)
Hi everybody, I'm trying to use g_velacc to calculate the diffusion
coeficient for my solute.
For this, I performed a simple simulation to test such tool.
1000 water molecules,
NPT ensemble
positions and velocities colected every 0.01ps
Gromacs 4.5.
However, once I run: g_velacc -f traj -s
Hi David,
Yes indeed, there are multiple ways to get a mol2 files besides using
chimera. You can get it from ZInc, or use openbabel or Marvin Sketch to
generate it, for example.
The result normally comes back within minutes. Are you sure you included
all hydrogens in the mol2 file? Sometime
You can also self assemble the bilayer around your peptide. There is a
tutorial on the Martini website for how to do this.
Cheers
Tom
On 12/10/10 21:02, Justin A. Lemkul wrote:
Sanku M wrote:
Hi,
I am using MARTINI coarse-grained force-field to study interaction of
a transmembrane pe
Sanku M wrote:
Hi,
I am using MARTINI coarse-grained force-field to study interaction of
a transmembrane peptide WALP or KALP in a lipid-bilayer. So,I was
planning to insert a martini KALP or WALP peptide inside a martini DPPC
bilayer in a transmembrane manner. For that purpose, I was go
Hi,
I am using MARTINI coarse-grained force-field to study interaction of a
transmembrane peptide WALP or KALP in a lipid-bilayer. So,I was planning to
insert a martini KALP or WALP peptide inside a martini DPPC bilayer in a
transmembrane manner. For that purpose, I was going through the MAR
Hi,
It works. Thanks a lot.
Sincerely,
Qian
- Original Message -
From: "Justin A. Lemkul"
Date: Wednesday, October 13, 2010 2:28 am
Subject: Re: [gmx-users] top file for two seperate peptides
To: Gromacs Users' List
>
>
> Qian Wang wrote:
> >Hi,
> > Thanks. Now I add TER after eve
Qian Wang wrote:
Hi,
Thanks. Now I add TER after every peptide coordinates. But then when I
used the command pdb2gmx -chainsep, it said "invalid command line
argument: -chainsep". So I am wondering the version I use is different
or something. My version is gromacs 4.0.7.
The -chainsep
Hi,
Thanks. Now I add TER after every peptide coordinates. But then when I used the
command pdb2gmx -chainsep, it said "invalid command line argument: -chainsep".
So I am wondering the version I use is different or something. My version is
gromacs 4.0.7.
Sincerely,
Qian
- Original Mess
Qian Wang wrote:
Hi,
I want to simulate two seperate peptids in one box. However, when I use
pdb2gmx to build the top file of this system, I found that gromacs
thought there is only one peptide because it added bond, angle and other
energy terms between the termius of these two peptides. I
Hi,
I want to simulate two seperate peptids in one box. However, when I use pdb2gmx
to build the top file of this system, I found that gromacs thought there is
only one peptide because it added bond, angle and other energy terms between
the termius of these two peptides. Is there any way to pr
On 2010-10-12 19.09, Michel Cuendet wrote:
Hi Ram,
Please note that the SwissParam parameters have been tested only with
the charmm force field. But this in principle shouldn't prevent you from
TRYING to use these parameters (which come from the Merck Molecular
Force Field in the first place)
Hi Ram,
Please note that the SwissParam parameters have been tested only with
the charmm force field. But this in principle shouldn't prevent you from
TRYING to use these parameters (which come from the Merck Molecular
Force Field in the first place) with OPLS.
The error you mention should
Hello Justin and Mark,
Thanks for the reply.
Reason that I didnt apply loop modelling was, for that region it is not given
in literature that, this region which consist of 10 residues will form a helix
of will remain in loop in an disorganized way. Therefore, I was reluctant in
doing loop recon
sonali dhindwal wrote:
Hello Sir,
I want to ask a question about missing residues, for which coordinates
are not defined in the PDB file.
I have this protein structure and in one of the loop there are some
residues whose coordinates are not defined in the file.
When I did pdb2gmx for prepari
ram bio wrote:
Dear Gromacs Users,
I have generated the topology and parameters files for my ligand
through swiss param site. Now i am trying to run a simulation of
protein ligand complex in POPC bilayer using OPLS force field in
Gromacs, but when I am using the grompp command in gromacs for t
NG HUI WEN wrote:
Dear gmxusers,
I have obtained a box of POPC with a starting dimension of 12.48, 12.36,
and 6.92 (nm) using genconf –nbox 2 2 1. The original lipid was
downloaded from Prof. Tieleman’s site (popc128a.pdb).
My intention is to equilibrate the new bilayer such that t
On 12/10/10 00:33, Mark Abraham wrote:
I have heard (read: read on random blogs here and there) that on
Intel compiling GROMACS with icc instead of gcc can bring up to
50% performance improvement.
If you are referring to this post
(http://kent-vandervelden.blogspot.com/2010/08/optimization-of-
- Original Message -
From: sonali dhindwal
Date: Wednesday, October 13, 2010 1:44
Subject: [gmx-users] query regarding missing residues
To: Discussion list for GROMACS users
---
| > Hello Sir,
>
> I want to ask a question about m
- Original Message -
From: "Justin A. Lemkul"
Date: Wednesday, October 13, 2010 0:50
Subject: Re: [gmx-users] output force - 2
To: Gromacs Users' List
>
>
> Петр Попов wrote:
> >
> >Is the way to decompose pull force?
> >
>
> None that I'm aware of. The only terms that (I think) ca
- Original Message -
From: "C. Batistakis"
Date: Wednesday, October 13, 2010 1:41
Subject: Re: [gmx-users] g_gyrate
To: Discussion list for GROMACS users
---
| > Dear Mark
> I will try to be more specific.
>
> In the case I have
Hello Sir,
I want to ask a question about missing residues, for which coordinates are not
defined in the PDB file.
I have this protein structure and in one of the loop there are some residues
whose coordinates are not defined in the file.
When I did pdb2gmx for preparing the topology, it joined
Dear Mark
I will try to be more specific.
In the case I have 4 chains in a simulation box, by typing g_gyrate -f traj.xtc
-s topol.tpr -nmol 4 I take the following:
Group 0 ( System) has 180elements
Group 1 ( AAA) has 45 elements
Group 2 ( BAA) has 45 e
Dear Gromacs Users,
I have generated the topology and parameters files for my ligand
through swiss param site. Now i am trying to run a simulation of
protein ligand complex in POPC bilayer using OPLS force field in
Gromacs, but when I am using the grompp command in gromacs for tpr
generation I am
Dear gmxusers,
I have obtained a box of POPC with a starting dimension of 12.48, 12.36, and
6.92 (nm) using genconf -nbox 2 2 1. The original lipid was downloaded from
Prof. Tieleman's site (popc128a.pdb).
My intention is to equilibrate the new bilayer such that the lipids,
particularl
Is it possible to slightly change the source code to adjust output of
pullf in appropriate form? And if it is, how?
Petr.
12 октября 2010 г. 17:49 пользователь Justin A. Lemkul
написал:
>
>
> Петр Попов wrote:
>>
>> Is the way to decompose pull force?
>>
>
> None that I'm aware of. The only ter
Петр Попов wrote:
Is the way to decompose pull force?
None that I'm aware of. The only terms that (I think) can be decomposed are
short-range nonbonded interactions, using energygrps.
You might be able to extract forces on subsets of atoms using g_traj, if you've
saved forces at suitab
For a homogenious system, you can also use g_density: g_density -sl 1
-dens mass -f -s -o
Mark Abraham wrote:
You get the density by running g_energy. If you've tried that and seen that the density wasn't there, that would be because your volume is constant in an NVT simulation. grompp pro
Is the way to decompose pull force?
2010/10/12 Justin A. Lemkul
>
>
> Петр Попов wrote:
>
>> Hello dear gmx-users!
>>
>> So, I run md and got all files md.cpt, .trr, .gro, mdf.xvg,... etc.
>> then I did: grompp_d -f sp.mdp -c md.gro -n index.ndx -p topol.top -o
>> sp.tpr
>> where sp.mdp differ f
You get the density by running g_energy. If you've tried that and seen that the
density wasn't there, that would be because your volume is constant in an NVT
simulation. grompp probably reported the density when you made the .tpr,
however.
Mark
- Original Message -
From: vferra...@unit
vferra...@units.it wrote:
Thanks a lot, but... How can I exctract density information by using
g_energy?
Have you tried it? You're given a list from which to choose. Type the number
of the property you want (i.e., Density), then either a blank line or the number
zero to terminate intera
Thanks a lot, but... How can I exctract density information by using g_energy?
Valerio
"Justin A. Lemkul" ha scritto:
Justin A. Lemkul wrote:
vferra...@units.it wrote:
I'm a GROMACS user and I want to authomatize solvent parametrization in
GROMOS force-field. The parametrization of a s
Justin A. Lemkul wrote:
vferra...@units.it wrote:
I'm a GROMACS user and I want to authomatize solvent parametrization in
GROMOS force-field. The parametrization of a solvent converg also on
the density. The problem is that g_density always ask on which element
of the system compute the dens
vferra...@units.it wrote:
I'm a GROMACS user and I want to authomatize solvent parametrization in
GROMOS force-field. The parametrization of a solvent converg also on
the density. The problem is that g_density always ask on which element
of the system compute the density and it is waiting for a
I'm a GROMACS user and I want to authomatize solvent parametrization in
GROMOS force-field. The parametrization of a solvent converg also on
the density. The problem is that g_density always ask on which element
of the system compute the density and it is waiting for a replay that
I can't authomat
Петр Попов wrote:
Hello dear gmx-users!
So, I run md and got all files md.cpt, .trr, .gro, mdf.xvg,... etc.
then I did: grompp_d -f sp.mdp -c md.gro -n index.ndx -p topol.top -o sp.tpr
where sp.mdp differ from md.mdp in one line: energygrps = Protein SOL
(in md.mdp: energygrps = System)
afte
I'm not sure what the problem is. If you want to merge groups to get the radius
of gyration over the union of those groups, then you need to use make_ndx on
your previous .ndx file to generate such a group.
Mark
- Original Message -
From: "C. Batistakis"
Date: Tuesday, October 12, 2010
Dear all
I have the following system. Substrate with 3696 particles and 4 polymer chains
with 45 beads/chain. After typing g_gyrate, I have the following option:
Group 0 ( System) has 680 elements
Group 1 ( ZZZ) has 500 elements
Group 2 ( AAA) has 45 eleme
Hi all,
I want to select waters in CNT using g_select.
g_select -f md.xtc -s md.tpr -sf selection.dat -os -oc -oi -om -selrpos
whole_mol_com -seltype whole_mol_com
selection.dat contains:resname SOL and ((x-1)^2+(y-1)^2<= 1) and (z
>=-0.7037 and z <= 0.6833 ). and an error occure,Readi
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