Hi all,
I would like to know if there is a
way by which we can get to know the coordinates of the centre of mass
for the molecule/system?
Since new to this fieldany suggestions would be of great help.
Thank you,
Annie Albin.
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gmx-users mailing
Dear all!
My Simulation was done in decane and dmso. during analysis(g_energy), i find
the energy of the whole system is positive
not negative.however, fluctuation of temperature ,pressure and total energy is
normal. Could anyone help me to figure out
whether this MD is normal or not!
Thank
Greetings once again fellow Gromacs-users,
I have seen a substantial and disturbing change in calculated free energy
differences
between systems run with Gromacs 3.3 and Gromacs 3.3.1. I am trying to
determine if
these differences are due to the new software, new parameters, insufficient
Hello,
Has anybody tried to use gromacs in parallel with the Intel Core Duo
macintoshes?
I installed gromacs and lam on some iMac with intel core duo
2x1.83GHz running the latest OSX with all updates.
I have everything working OK but the scaling is very inefficient.
Here are the results of
Dear gmx-users We want to study interaction of ligand to enzyme. We constructed the gro and top file from Prodrg and add it to the end of enzyme gro and change the number of atoms. Some of calculation carried out until mdrun of pr.mdp, but in this step we encontered to following error. what is the
Hello GROMACS community,
I was wondering if somebody could walk me through the process of
calculating lipid order parameters (for a DMPC membrane), using the
g_order analysis tool?
I've got a 5 ns trajectory and would like to make one of the classic
order parameter plots:
i.e.
On the
Dear gromaxers, I havea system of 6500 atoms. Gromacs shows that the
simulation will take 8 hrs to complete the simulation. Is my system
that large? The system is 15x15x15 units cells of Fe. so the the total
box size is 4.305. I have tken cu-offs for LJ as 1.55. There is only LJ
interaction.
Does this give any clue. It shows large PE, KE and temp. Could that be a reason? More information required?
However, I have chenged my system a bit. My conf.gro file has just 2
atoms. one at the origin and the other at the body center. I use
genconf to create a mesh of 4x4x4 unit cells at a
During the ./configure of gromacs on my Cygwin Bash Shell, I get the
following error:
configure: error: Cannot find fftw3f library
I have installed fftw3, but evidently not to the satisfaction of
gromacs. I put the fftw3.h in usr/local/include, and that enabled me to
make it past the
I previously posted my modifications to get POPE to work with OPLSAA. You could
make the analogous changes to your system. The message was:
[gmx-users] lipid.itp LJ-1,4 values involving water
Wed May 3 20:44:51 CEST 2006
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gmx-users mailing list
I have a simulation box with a polymer in the middle
and solvent molecules surrounding it. The box ended
up being much bigger than needed--I'll need to reduce
its size from 20.0 nm to 15 nm, removing solvent
molecules in the process. Is there a way to do this?
Thanks.
Gil Claudio
Ralf B. Lukner wrote:
During the ./configure of gromacs on my Cygwin Bash Shell, I get the
following error:
configure: error: Cannot find fftw3f library
I have installed fftw3, but evidently not to the satisfaction of
gromacs. I put the fftw3.h in usr/local/include, and that enabled me to
karamyog singh wrote:
Does this give any clue. It shows large PE, KE and temp. Could that be a
reason? More information required?
Your PE is ridiculously large. You have order 10^5 kJ/mol of PE for
every atom, and obviously that is only coming from your LJ function.
Check how you generated
Hi Davood,Although there could be many causes, in this case I'd suspect that there is a water molecule trapped inside the protein. This can be the result of solvation using genbox. An isolated water molecule can start to rattle. It will get close to one side of the microcavity and kicked to the
karamyog singh wrote:
Dear gromaxers, I havea system of 6500 atoms. Gromacs shows that the
simulation will take 8 hrs to complete the simulation. Is my system that
large? The system is 15x15x15 units cells of Fe. so the the total box
size is 4.305. I have tken cu-offs for LJ as 1.55. There is
Hi freinds
I try to use make_hole program to make a hole in popc
and input ion channel in it.whould you please help me?
mahbubeh
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Can somebody post the particulars for how they submit a parallel run on their
system along with the brand/version of MPI they use?
Thanks everyone for recent help with parallel run hanging/crashing. I have
determined that it must be a problem with the way that I am submitting the
parallel job
Title: FW: Position restrain
Hi gmx-users
While running a MD of PE with position restrain, i get this error message
Fatal error: [ file posre.itp, line 6 ]:
Atom index (101) in position_restraints out of bounds (1-12)
My atom index goes up to 6000, why do I have to be in the 1-12 range?
Ralf B. Lukner wrote:
During the ./configure of gromacs on my Cygwin Bash Shell, I get the
following error:
configure: error: Cannot find fftw3f library
I have installed fftw3, but evidently not to the satisfaction of
gromacs. I put the fftw3.h in usr/local/include, and that enabled me
to
Hello GROMACS community,
I was wondering if somebody could walk me through the process of
calculating lipid order parameters (for a DMPC membrane), using the
g_order analysis tool?
I've got a 5 ns trajectory and would like to make one of the classic
order parameter plots:
i.e.
On the y-axis:
Dear Gromacs users,
I am tring to bulid ligand topology using OPLSAA forcefield. I want to know
that should i user pair interactions in the ligand topology. If yes what is
criteria for chosing atom pairs for pair interactions
with thanks
teje
___
[EMAIL PROTECTED] wrote:
On Mark Abraham's suggestion I verified that mpirun isn't a local wrapper.
However, he also suggested mpirun may not play nicely with a single-processor
script that subsequently runs an MPI child process. I forwarded this to our lab
tech who was unsure what this meant
4tejender wrote:
Dear Gromacs users,
I am tring to bulid ligand topology using OPLSAA forcefield. I want to know
that should i user pair interactions in the ligand topology. If yes what is
criteria for chosing atom pairs for pair interactions
I've no idea what you mean by user pair
linfu wrote:
Dear all!
My Simulation was done in decane and dmso. during analysis(g_energy), i find
the energy of the whole system is positive
not negative.however, fluctuation of temperature ,pressure and total energy
is normal. Could anyone help me to figure out
whether this MD is
hi friends,
I am installing GMX on a 2xdual core opteron processor system running on linux 10.0
I install lam by disabling the fortran as
./configure -without-fc
make
make install
I configure fftw
./configure --enable-floats --enable-mpi
make
make install
distclean
./configure --enable-mpi
It seems like reference #34 in the GMX 3.3 manual should be:
Levitt, M., Sander, C. and Stern PS. The normal modes of a protein: native
bovine pancreatic trypsin inhibitor. Internatl. J. Quant.Chem., Quantum Biology
Symposium 10, 181-199. 1983
And not as written.
Ran.
--
However if the gen_velocity breaks up my system and at the end of my
simulation, I do not get a bcc structure at lets say 273 K, which I am
not getting, then how can I consider my simulation to be correct? The
structure should remain the same. Or could it be that since my
structure is a nano layer
karamyog singh wrote:
However if the gen_velocity breaks up my system and at the end of my
simulation, I do not get a bcc structure at lets say 273 K, which I am
not getting, then how can I consider my simulation to be correct? The
structure should remain the same.
I don't get the
Dear Gromacs list members,
Is it possible to choose best force field to
extract bond constants to reevaluate them into Morse potential
parameters?
D. Egorov, USMA, Yekaterinburg,
Russia.
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gmx-users mailing listgmx-users@gromacs.org
Title: Position restrain
While running a MD of PE with position restrain, i get this error message
Fatal error: [ file posre.itp, line 6 ]:
Atom index (101) in position_restraints out of bounds (1-12)
My atom index goes up to 6000, why do I have to be in the 1-12 range?
Regards
You're on your own here unless you can provide more information.
here is my .mdp file too.
-
karamyog.
title = Yo
cpp
= /usr/bin/cpp
include =
define =
integrator = md
tinit = 0
dt
Егоров Д.А. wrote:
Dear Gromacs list members,
Is it possible to choose best force field to extract bond constants to
reevaluate them into Morse potential parameters?
It depends what you want to use the potential for, and it is probably a
bad idea. The bond constants are members of a
From: [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: gmx-users@gromacs.org
Subject: [gmx-users] TI, sampling, sc_power, and sc_alpha
Date: Fri, 26 May 2006 12:36:20 -0700 (PDT)
Greetings once again fellow Gromacs-users,
I have seen a substantial and
Hello GROMACS community,
I was wondering if somebody could walk me through the process of
calculating lipid order parameters (for a DMPC membrane), using the
g_order analysis tool?
I've got a 5 ns trajectory and would like to make one of the classic
order parameter plots:
i.e.
On the y-axis:
My take is that it is preferable to partition your vdW and charge
changes into two separate calculations, as the soft core settings that
work well for the vdW portion make the charging portion a more
difficult transformation than normal, and the settings that work
well for charging make the vdW
Do you mean, use pair interactions? If you're referring to the [
pairs ] section of your topology, well, you will probably need to look
at details on the force field to see what it expects, as the answer to
this is force field dependent, and I don't typically use OPLS-AA. The
[ pairs ] section is
linfu wrote:
Dear all!
My Simulation was done in decane and dmso. during analysis(g_energy), i find
the energy of the whole system is positive
not negative.however, fluctuation of temperature ,pressure and total energy is
normal. Could anyone help me to figure out
whether this MD is normal or
Yiannis wrote:
Hello,
Has anybody tried to use gromacs in parallel with the Intel Core Duo
macintoshes?
I installed gromacs and lam on some iMac with intel core duo 2x1.83GHz
running the latest OSX with all updates.
I have everything working OK but the scaling is very inefficient. Here
are
Hi All,thanks to Steffan , Jim and Kaushal for helping me out in the POPC simulation setup. i finally got everything to work. i guess the imp thing was to change the POPC to POP in .top file. thanks once again.Arindam Ganguly
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gmx-users mailing list
Ran Friedman wrote:
It seems like reference #34 in the GMX 3.3 manual should be:
Levitt, M., Sander, C. and Stern PS. The normal modes of a protein: native
bovine pancreatic trypsin inhibitor. Internatl. J. Quant.Chem., Quantum
Biology
Symposium 10, 181-199. 1983
And not as written.
Ran.
I try to use make_hole program to make a hole in popc
and input ion channel in it.whould you please help me?
Try a search of this emailing list, which you do via the website.
Details on how to do this have been metioned a few times.
I have no idea how it is done and have never done it myself,
Prof. Van Der Spoel,
Regarding your suggestion here: Where exactly are lines 579 and 580
that one must modify? (I'm having this same error)
Thanks,
Arneh
David van der Spoel wrote:
Sukit Leekumjorn wrote:
Dear GMX users,
I have encounter some problem with g_order in Gromacs3.3.1. I
Hi Pedro, thank you for your prompt reply.
I'm attempting to do what you suggested.
1). I create an index file, called sn2.ndx, which contains 14 groups,
one group for each carbon type in the chain (labeled C2A, C2B, . . . C2N).
2) I then try to execute the following command:
g_order -f
Alessandro Mattozzi wrote:
While running a MD of PE with position restrain, i get this error message
Fatal error: [ file posre.itp, line 6 ]:
Atom index (101) in position_restraints out of bounds (1-12)
My atom index goes up to 6000, why do I have to be in the 1-12 range?
your
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