Eric Shamay wrote:
Dear gromacs community,
I've been trying to switch over from AMBER and I'm running into a few
issues that the manual doesn't clarify well enough for me. Can anyone
point me to information on adding in polarizability to atoms? In amber
it was a simple matter of adjusting the
JMandumpal wrote:
Dear David,
I didn't get the desired box length when I tried to use editconf command
( I took the tip5p box from gromacs/tutor directory) . Then, I tried
editconf command to generate .gro file using myown water box. It worked!!
Still, there is a problem. How can I create
Hi,
I am new to Gromacs. I am following this tutorial:
http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/index.html. My
question is: why it has multiple steps of energy minimization and
position restrained simulation? Is that a common practice? What's the
key difference among these steps?
Than
Hi,
How to specify the .mdp file in order to run position restrained
simulation? From the examples I found on the internet, it seems that
the only difference between the .mdp file for position restrained
simulation and the one for actual MD simulation is the simulation time
-- the position restrai
Dear David,
I didn't get the desired box length when I tried to use editconf command ( I
took the tip5p box from gromacs/tutor directory) . Then, I tried editconf
command to generate .gro file using myown water box. It worked!!
Still, there is a problem. How can I create .ndx file?- I tried
Thank all of you for the suggestions!
I then ran the procedures described at
(http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/index.html),
where it adds water before energy minimization, and it also has
position restraint step. But when I came to the step:
grompp -f dyna/pr1_SOLV.mdp -po X_p
Eric Shamay wrote:
Dear gromacs community,
I've been trying to switch over from AMBER and I'm running into a few
issues that the manual doesn't clarify well enough for me. Can anyone
point me to information on adding in polarizability to atoms? In amber
it was a simple matter of adjusting the
i see. i reran the trajectory with reaction field electrostatics and that
gave a more negative energy value which was closer to what i was expecting.
i guess the missing reciprocal space contributions explains this
discrepancy.
is there a way to get the full interaction energy with PME ?
thnx fo
Dear gromacs community,
I've been trying to switch over from AMBER and I'm running into a few issues
that the manual doesn't clarify well enough for me. Can anyone point me to
information on adding in polarizability to atoms? In amber it was a simple
matter of adjusting the frcmod file, but I can'
Chris Borchert wrote:
Hello. I'm trying to get a MPI GROMACS 3.3.2 build for a Cray XT3 (AMD Opteron cluster). The compute pool runs a
linux microkernel called Catamount. You compile for Catamount with "cc" or 'ftn", and launch a job
with "yod". I'm getting a "cannot compute sizeof int" error f
Hello. I'm trying to get a MPI GROMACS 3.3.2 build for a Cray XT3 (AMD Opteron
cluster). The compute pool runs a linux microkernel called Catamount. You
compile for Catamount with "cc" or 'ftn", and launch a job with "yod". I'm
getting a "cannot compute sizeof int" error from configure. Here is
/ I'm performing a transmembrane protein simulation in an explicit DPPC
/>/ bilayer. I manually removed the lipids to accomodate my protein and the
/>/ system has undergone 15 ns of equilibration.
/>/
/>/ In removing the lipids, I a gap betwteen the protein and membrane
/>/ resulted. Most of th
The length of your simulation is irrelevant, the frequency of frame output is.
If you don't output frames at least 5x per picosecond, asking for the frames in
a 0.1ps gap is not going to produce an output - because there probably won't be
any. Check your mdp.
- Original Message
From:
What I meant is: do you save the trajectory every 0.1ps?
The problem seem to be that trjconv isn't able to find any frame between
t=0.1ps and t=0.2ps. So, if you save you data every 1ps, there's no data
in your .xtc file. This is why Xavier suggested to use gmxcheck, that
will tell you both how ma
Of course, I am performing a 40 ns simulation, and 14 ns of it has been
finished.
What may be the problem? I know, I can extract specific frames via VMD, but it
changes atom types after saving in pdb format.
-Original Message-
From: Ran Friedman <[EMAIL PROTECTED]>
To: Discussion list
I see. Do you have any structure between t=0.1ps and t=0.2ps?
Ran.
OZGE ENGIN wrote:
> The command line ws the following:
>
> trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb
>
>
___
gmx-users mailing listgmx-users@gromacs.org
The command line was the following:
trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb
-Original Message-
From: Ran Friedman <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Mon, 19 Nov 2007 17:10:51 +0100
Subject: Re: [gmx-users] trjconv does not work
De
The command line ws the following:
trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb
-Original Message-
From: Ran Friedman <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Mon, 19 Nov 2007 17:10:51 +0100
Subject: Re: [gmx-users] trjconv does not work
Dea
On Mon, 19 Nov 2007 18:02:31 +0200
"OZGE ENGIN" <[EMAIL PROTECTED]> wrote:
Hi all,
I want to extract some frames from the whole trajectory. So, I used -trjconv
with (b) and (e) options.
P.S: I use the Gromacs 3.3.1 version.
But I got the following error:
Select a group: 0
Selected 0: 'Syst
Dear Ozge,
What was the command line exactly?
Ran.
OZGE ENGIN wrote:
> Hi all,
>
> I want to extract some frames from the whole trajectory. So, I used -trjconv
> with (b) and (e) options.
>
> P.S: I use the Gromacs 3.3.1 version.
>
> But I got the following error:
>
> Select a group: 0
> Select
Hi all,
I want to extract some frames from the whole trajectory. So, I used -trjconv
with (b) and (e) options.
P.S: I use the Gromacs 3.3.1 version.
But I got the following error:
Select a group: 0
Selected 0: 'System'
Last frame -1 time0.000
Precision of traj.xtc is 0.001 (nm)
W
Hi all,
I want to extract some frames from the whole trajectory. So, I used -trjconv
with (b) and (e) options.
P.S: I use the Gromacs 3.3.1 version.
But I got the following error:
Select a group: 0
Selected 0: 'System'
Last frame -1 time0.000
Precision of traj.xtc is 0.001 (nm)
W
If the water is already in the gap, delete it, or move it out of the bilayer.
What I meant was: If you start the equilibration all over again, try
increasing the force constants of the restraints on water along the
bilayer normal.
On 19 Nov 2007 11:52:49 +, N-J.M. Macaluso <[EMAIL PROTECTED
Do you mean constrain the force constants just in the z-direction? Keep in
mind that the water is already in the gap, so it's now a matter of getting
it out. Would constraining water in any direction accomplish this?
Thanks,
Max
On Nov 19 2007, himanshu khandelia wrote:
I already constrain
Quoting liang <[EMAIL PROTECTED]>:
> > Never couple solvent and ions separately. Check out:
>
> > http://wiki.gromacs.org/index.php/Thermostats
>
> > Try tc-grps = Protein Non-protein
>
> excuse me, if the system includes lipid bilayer, how should i set the
> tc-prgs?
> Protein + Lipids + Sol and
Thanks for your response,
I'm sorry, but I didn't find any text on the "membrane simulation" page on
the wiki. What I meant by constraining waters in the z-direction is that at
the start of the simulation, I constrained waters in the z-direction so
that they wouldn't fall into the gap between
> I already constrained the waters in the z-direction
> at the start of the simulation, so that didn't work in this case.
This happened to me as well. Try increasing the force constants on
water by an order of magnitude.
___
gmx-users mailing listgm
N-J.M. Macaluso wrote:
Hi,
I'm performing a transmembrane protein simulation in an explicit DPPC
bilayer. I manually removed the lipids to accomodate my protein and the
system has undergone 15 ns of equilibration.
In removing the lipids, I a gap betwteen the protein and membrane
resulted. M
Hi,
I'm performing a transmembrane protein simulation in an explicit DPPC
bilayer. I manually removed the lipids to accomodate my protein and the
system has undergone 15 ns of equilibration.
In removing the lipids, I a gap betwteen the protein and membrane resulted.
Most of the lipid molecul
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