Please post again, this time turn off your html formatting in your
email. It is too difficult for me to read with all of the
characters.
Also, please be more explicit about what the problem is. Is your area
per lipid too small? It seems that way, but I did not use DMPC myself.
I use POP
Anamika Awasthi wrote:
> shall we mention in this way?
> steps:
> 1- tpbconv -f old.trr -e old.edr -s old.tpr -o new.tpr
> 2- mdrun -v -deffnm new.tpr
As "mdrun -h" tells you, "-deffnm xxx" sets the default filename for all
file options. What it doesn't say is that it sets the default fil
> shall we mention in this way?
> steps:
> 1- tpbconv -f old.trr -e old.edr -s old.tpr -o new.tpr
> 2- mdrun -v -deffnm new.tpr
hello Sudheer.
As i know about this command, this is only a shortcut and it takes all the
filename as default,
so if we will do mdrun after a second or third crash, all
ANINDITA GAYEN wrote:
I have suffering from a problem with dmpc bilayer simulation at 300K
with oplsaa-berger combination that is showing area of 50nm2 after 1.5
ns from g_energy and g_traj.
Is this the problem? If so, then you need to tell us what you're
expecting and why. Is the number con
I have suffering from a problem with dmpc bilayer simulation at
300K
with oplsaa-berger combination that is showing area of 50nm2 after 1.5
ns from g_energy and g_traj. I have used half-epsilon double pairlist
method. the itp and mdp files are attached with. However editconf again
showing the corre
David Huang wrote:
hi
i'm new to gromacs and am trying to construct an initial configuration
for a system of polymer chains. i've looked through previous posts to
the mailing list (such as the one attached below) and read chapter 5
of the gromacs manual and the wiki, but it is still not clear to
I guess you have not listed all the dihedrals in the configuration of a ethanol
molecule.
In your .top file, there are only two dihedrals, you might need to include all
others.
By the way, check the other part of your topology to avoid other incorrect
inputs.
Best regards.
Yue Shao
silve
On Tue, 2008-05-13 at 20:32 +0300, Jussi Lehtola wrote:
> On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote:
> > First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if
> > it looks reasonable.
> >
> Thanks, using the vacuum method I seem to get better results.
It seems
hi
i'm new to gromacs and am trying to construct an initial configuration
for a system of polymer chains. i've looked through previous posts to
the mailing list (such as the one attached below) and read chapter 5
of the gromacs manual and the wiki, but it is still not clear to me
how to construct
Well, the end caps contain a few pentagons so the angle terms for
those atoms would have to change from the normal 120 degrees used for
hexagons. Other than that, I don't think the force field parameters
would have to change. What do you mean by the tube "breaking apart"?
That sounds like you don't
On Tue, 2008-05-13 at 14:34 +0100, Kukol, Andreas wrote:
> First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if it
> looks reasonable.
>
> You could also have a look at the definition of ETHH in the GROMOS96
> forcefield, e.g. in ffG43a2.rtp. Although this is a united atom
Quoting Thomas Schlesier <[EMAIL PROTECTED]>:
*snip*
> The .itp file for the ohter molecule (the alkane chain is 4 atoms longer)
> looks really the same but the charges are a little bit different.
> So, have i done this right, or are there any mistakes (expect for the charge,
> see below)?
>
> On
First of all, thanks for the answers.
So, i get my coordinate-file from the prodrg-beta server (with the gromos96
force field; ffG534a1). This file i edited so that it looks like the format of
a .g96 file:
TITLE
linker ohne benzol
END
POSITION
1 ZUG CAA14.9185833936.1435418
Hi everybody,
I have a big problem about the usage of the command do_dssp. Ok, I have
downloaded the file dsspcmbi from this link
ftp://ftp.cmbi.ru.nl/pub/molbio/software
Of course, I have sended the license fax before. After I downloaded the
file I renamed it simply as dssp and I copied that in
Dear Berk Hess,
I am Cristina Greco. When I first wondered why there were no multiple or
adaptive timestep methods implemented I suspected that the reasons had to do
with compatibility with other options.I was just interested because I want to
set up a simulation to study problems connected wi
First try the EM/MD of 1 molecule in vacuum ('ethanol-gas') and check, if it
looks reasonable.
You could also have a look at the definition of ETHH in the GROMOS96
forcefield, e.g. in ffG43a2.rtp. Although this is a united atom topology it
might give you clues, if something is wrong.
Andreas
Date: Tue, 13 May 2008 12:51:57 +0200
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] multiple time step algorithm
Berk Hess wrote:
It would also make the code more
complicated than it already is.
Berk.
It may be useful to incorporate these th
David van der Spoel wrote:
> Ran Friedman wrote:
>> Berk Hess wrote:
>>> It would also make the code more complicated than it already is.
>>>
>>> Berk.
>> It may be useful to incorporate these things as part of the source
>> but to compile them only if requested by the user, as done e.g. in
>> so
Ran Friedman wrote:
Berk Hess wrote:
It would also make the code more complicated than it already is.
Berk.
It may be useful to incorporate these things as part of the source but
to compile them only if requested by the user, as done e.g. in some
features of charmm. This will make the main
Quoting Peyman Yamin <[EMAIL PROTECTED]>:
> Dear gromacs users,
>
> I'm trying to simulate amphiphilic molecules, building stable
> structures by non-bonded interactions. I have seen in biological research,
> membranes and proteins therein are often subject of simulations. A cell
> membrane, I gue
Berk Hess wrote:
> It would also make the code more complicated than it already is.
>
> Berk.
It may be useful to incorporate these things as part of the source but
to compile them only if requested by the user, as done e.g. in some
features of charmm. This will make the main code only minimally mo
Hi,
I like the idea of having multiple time step in gromacs, but many
analysis tools would need a lot of rewriting, which would require more
work than changing mdrun. Or am I wrong?
Berk Hess skrev:
Hi,
Our philosophy up till now has been to remove the fastest motions
(using constraints and
Hi,
I have constructed topologies for methanol, ethanol, propanol and
butanol using x2top with the atomic coordinates from NIST Chemistry
WebBook. I have modified the topologies by putting the CH3s, CH2s and
OHs in their separate charge groups.
Now I have run into problems when trying to minimi
Hi,
Our philosophy up till now has been to remove the fastest motions
(using constraints and virtual sites) allowing for a larger time step,
instead of using a multiple time step algorithm.
Having a multiple time step algorithm would be nice, but this
would cause a lot more communication in the p
Dear David,
Recently we have developed hybrid or Hamiltonian REMD method by
modifying gromacs source code. If interested see our two JCP papers.
If you, developers of GROMACS, are interested in including such method
in new version of gromacs release. I am very pleased to share the idea
here:
In R
Dear David av der Spoel
Thanks for answering. I was just curious to know why you chose not to implement
them.
Have a nice day
On Tue, 13 May 2008 12:00:43 +0200, David van der Spoel said:
>
> Cristina GRECO wrote:
> > Dear Gromacs users and developers,
> >
> > it seems to me that Gromacs does
Cristina GRECO wrote:
Dear Gromacs users and developers,
it seems to me that Gromacs does not allow for multiple time step nor adaptive
timestep MD. Is that correct or did I miss something? If that's true what's the
reason ? For example, would there be problems in running such algorithm in
p
Dear Gromacs users and developers,
it seems to me that Gromacs does not allow for multiple time step nor adaptive
timestep MD. Is that correct or did I miss something? If that's true what's the
reason ? For example, would there be problems in running such algorithm in
parallels?
Thanks to all
Dear gromacs users,
I'm trying to simulate amphiphilic molecules, building stable
structures by non-bonded interactions. I have seen in biological research,
membranes and proteins therein are often subject of simulations. A cell
membrane, I guess, could be an example of a structure built not by
Hi,
I want to simulate the ethanol system, and I generate the .itp and .gro files
of ethanol by myself. At first, I take the ethanol as solute and create the box
and add water into it, everything is ok. But when I take ethanol as solvent,
create an box with an organic name as tob and try to fill
On Tue, 13 May 2008 13:21:12 +0530
"sudheer babu" <[EMAIL PROTECTED]> wrote:
shall we mention in this way?
steps:
1- tpbconv -f old.trr -e old.edr -s old.tpr -o new.tpr
2- mdrun -v -deffnm new.tpr
check (gmxcheck -h) the content of trr and edr files!
.trr should contain coordinates and velociti
Dear Serdar,
you can find the option for reading every nth frame in VMD (default is
zero, meaning every frame), when loading the xtc-file into the molecule.
If you want to analyse the trajectory and the tool runs out of memory,
there is also the possibility to analyze the whole file part by part
shall we mention in this way?
steps:
1- tpbconv -f old.trr -e old.edr -s old.tpr -o new.tpr
2- mdrun -v -deffnm new.tpr
Thanks in advance.
On Mon, 12 May 2008 15:10:32 +0530
"Anamika Awasthi" <[EMAIL PROTECTED]> wrote:
> Dear Friends,
>If my simulation crashed because of power failure,
Yes, that's exactly what the first reply was telling you. The option is
"stride", I believe.
- Original Message
From: serdar durdagi <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Tuesday, May 13, 2008 8:44:37 AM
Subject: Re: [gmx-users] cutting the trajectory in smal
Dear Florian,
I want to analyze, trajectory files. So, I need all frames.
by the way, in VMD is there any option to use every 10th or 20th frame?
Thanks
Serdar
Florian Dommert <[EMAIL PROTECTED]> schrieb:
serdar durdagi wrote:
> Dear all,
>
> I made a simulation with 2
Use -b and -e options repeatedly to save part of your trajectory into a series
of files
OR: use '-skip 2' to reduce the number of frames by half over the whole of your
simulation.
Andreas
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of serdar durdagi
Sent: 13 May 2008 08:16
To:
serdar durdagi wrote:
> Dear all,
>
> I made a simulation with 2.5 ns (with 12500 frames), when I want to
> open this *.xtc file in VMD, it fails. it can read around 50% of
> frames and than complains low virtual memory (actually I am using a PC
> that has 1GB RAM).
Hello,
if you just want to
Dear all,
I made a simulation with 2.5 ns (with 12500 frames), when I want to open this
*.xtc file in VMD, it fails. it can read around 50% of frames and than
complains low virtual memory (actually I am using a PC that has 1GB RAM).
Thus, I would like to cut my *.xtc file to small su
38 matches
Mail list logo
