Hi Fabricio,
It's not correct to change your value of alpha, you should use a single value
for the whole transformation. The soft core potential is constructed so that
the end points at lambda=0 and 1 represent the 'native' states (with no
influence from the soft core parameters), and that
Dear users,
Recently, I encounter a very strange thing while perfoming MD using GROMACS.
With the same minimization parameters, mdrun can generate different
configuration in parallel way or not. It seems that the former one leads to
obvious exploding of the configuration into parts whereas
Hello,
You can try VMD. I is able to write coordinates in a lot of format,
including the dcd and crd ones. Both are readable by ptraj, I believe.
Otherwise, you can have a look on OpenBabel. Be careful when you convert
you trajectory into the Amber format. You probably have to include the box
Chaofu,
What implementation of mdrun do you use? What system concretely do you
energy-minimize? What do you mean by saying exploding of the
configuration into parts?
Vitaly
Dear users,
Recently, I encounter a very strange thing while perfoming MD using GROMACS.
With the same minimization
-- Dear All,
I am getting the following error:
Killed by signal 2
Killed by signal 2
Killed by signal 2
Killed by signal 2
Killed by signal 2
Killed by signal 2
Killed by signal 2
Killed by signal 2
.
.
.
.
Killed by signal 2
, when i am submitting a job with GROMACS (using
Hi everybody,
I'm trying to run simulations with a charge distribution within one single
atom. Is there a way to create a molecule, in which every atom has a charge
distribution - more charge points at one atom.
Is it possible to run a simulation in a polarizable electric continuum in stead
From: rolf.is...@rwth-aachen.de
To: gmx-users@gromacs.org
Date: Tue, 11 Aug 2009 12:14:12 +0200
Subject: [gmx-users] many charges within one atom
Hi everybody,
I'm trying to run simulations with a charge distribution within one single
atom. Is there a way to create a molecule, in
On Aug 11, 2009, at 11:52 AM, BSV Ramesh wrote:
-- Dear All,
I am getting the following error:
Killed by signal 2
Killed by signal 2
Killed by signal 2
Killed by signal 2
Killed by signal 2
Killed by signal 2
Killed by signal 2
Killed by signal 2
.
.
.
.
Killed by signal 2
,
Thank you for the article.
Nancy
On Mon, Aug 10, 2009 at 9:34 PM, Dallas B. Warren
dallas.war...@pharm.monash.edu.au wrote:
You might want to consider the parameters I developed for propylene
glycol http://dx.doi.org/10.1021/mp8001667 ... might provide some
guidance for you in terms
Dear all,
i
want to simulate a protein solvated in water. I have downloaded the
protein coordinate from RCSB protein data bank (ID 2KB7).
These has 20 merged coordinate i have taken conformer #6. Then i
run pdb2gmx with ffG43a1 solvate the protein with spc waters.
Next i energy
Moutusi Manna wrote:
Dear all,
i
want to simulate a protein solvated in water. I have downloaded the
protein coordinate from RCSB protein data bank (ID 2KB7).
These has 20 merged coordinate i have taken conformer #6. Then i
run pdb2gmx with ffG43a1 solvate the protein with spc
Hi Floris. So what you mean is that I should either use soft core for
the entire transformation or not use it at all. But then I do not
understand what Carsten said about using at least on lambda values
close to 0 and 1. I thought that if I used soft core on the last point
of my transformation
Hi Justin,
Is there any information on the gmx-website that explains how I should do
that? Does the tip means I should separate my original structure and the
groups that I attached to it??/ Many Thanks/Jamie
On Mon, Aug 10, 2009 at 9:31 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Jamie Seyed
Jamie Seyed wrote:
Hi Justin,
Is there any information on the gmx-website that explains how I should
do that? Does the tip means I should separate my original structure and
the groups that I attached to it??/ Many Thanks/Jamie
Please see the manual, section 4.6.2. I don't know what you
Hi Justin,
I read the section 4.6.2, so according to the section I should have groups
with 0 charge, so I assigned each ch3 (total charge=0) for cgnr the same
number. I still get the same Note. Should I assigned the same number for all
atoms to cgnr in the atom section of itp-file?? In this way my
Jamie Seyed wrote:
Hi Justin,
I read the section 4.6.2, so according to the section I should have
groups with 0 charge, so I assigned each ch3 (total charge=0) for cgnr
Charge groups, in general, should at least have integer charge (i.e.,
carboxylate in an ASP side chain), but yes, zero
Hallo
Maybe try
comm-grps = protein all-but-protein
(all-but-protein being all atoms except those contained in protein)
I guess this problem is brought about by the way VCM groups are constructed:
src/kernel/readir.c, do_numbering(), line 1081 in 4.0.3
if (grps-nr == 1) {
Dear Gromacs Users,
I have downloaded xdr library to read .xtc files.
The installation of the xdrlibrary worked without any problems. The
compilation of the test program trr2xtc.c also worked.
Now I'm trying to store the coordinates of a xtc trajectory into a local
variable. I first tried
mohit kumar wrote:
; DPPC itp file
; Use ffG43A1-S3 parameter files
There's nothing obviously wrong with this topology. Are you using your own
modified version of ffG43a1? If so, the problem may lie in the [ pairtypes ]
directive in the force field file, not this .itp file.
-Justin
;
Dear GROMACS Gurus,
I assigned improper dihedrals to my graphene structuure but still see it
vibrating. Is this to be expected? I thought the purpose of improper
dihedrals was to keep planar structures planar.
Here is a copy of a couple of sections of my topology file after
assigning the
Darrell Koskinen wrote:
Dear GROMACS Gurus,
I assigned improper dihedrals to my graphene structuure but still see it
vibrating. Is this to be expected? I thought the purpose of improper
dihedrals was to keep planar structures planar.
There is still a force constant associated with the
Hi Lipi,
What do you mean saying that the coordinates are random?
You can access the coordinates of the particular atom with
x_xtc[i][j], where i is a number of atom in a system, j[0] - is
x-coord, j[1] - y-coord, j[2] - z-coord. The same logic relates to
reading trr files.
Vitaly
I have
On the same topic, I have a question to the community: does anybody
try to make *so*-library (or *dll* on windows) of xdrfile in order to
use with other programming languages? I spent a day trying to master
this art but didn't still succeed. If somebody more experienced with
dynamic libraries than
Yes, many people have encountered this problem with mpich 1.2.7 Use a
version of MPICH2 (like OpenMPI) v1.3
Jim
-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Andrew Paluch
Sent: Monday, August 10, 2009 10:53 AM
To:
On Tue, 2009-08-11 at 23:22 +0300, Vitaly V. Chaban wrote:
On the same topic, I have a question to the community: does anybody
try to make *so*-library (or *dll* on windows) of xdrfile in order to
use with other programming languages? I spent a day trying to master
this art but didn't still
Dear all,
I performed an md simulation but it crashed at the beginning because
according to it system was exploding. Also when I tried to see the system
by ngmx, there was no water anymore and it was only the molecule sitting in
the box(after grompp and before mdrun it was a box of water plus the
Jamie Seyed wrote:
Dear all,
I performed an md simulation but it crashed at the beginning because
according to it system was exploding. Also when I tried to see the
system by ngmx, there was no water anymore and it was only the molecule
sitting in the box(after grompp and before mdrun it
Jamie Seyed wrote:
Dear all,
I performed an md simulation but it crashed at the beginning because
according to it system was exploding. Also when I tried to see the system
by ngmx, there was no water anymore and it was only the molecule sitting in
the box(after grompp and before mdrun it was a
Dear Mark and Vitaly,
In order to get help, here I describe the more detailed procedure.
I successfully generated the gro and top files using pdb2gmx.
pdb2gmx -f -o -p -ter
And also the grompp finished successfully.
grompp -f -c -p -o
Then I ran the mdrun in parallel way, only to
So what you mean is that I should either use soft core for
the entire transformation or not use it at all. But then I do not
understand what Carsten said about using at least on lambda values
close to 0 and 1. I thought that if I used soft core on the last point
of my transformation (the one that
Dear GROMACS Gurus,
In my simulation of a graphene structure surrounded by an ammonia gas, I
am not seeing any adsorption of the ammonia molecules onto the surface
of the graphene structure. I am wondering if the reason I am not seeing
any absorption is because the graphene lattice is
wuxiao wrote:
Dear Mark and Vitaly,
In order to get help, here I describe the more detailed procedure.
I successfully generated the gro and top files using pdb2gmx.
pdb2gmx -f -o -p -ter
And also the grompp finished successfully.
grompp -f -c -p -o
Then I ran the mdrun in
Darrell Koskinen wrote:
Dear GROMACS Gurus,
In my simulation of a graphene structure surrounded by an ammonia gas, I
am not seeing any adsorption of the ammonia molecules onto the surface
of the graphene structure. I am wondering if the reason I am not seeing
any absorption is because the
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