I am very new to this MD simulation, by reading the tutorials in the
website I have run an simulation and it is running from last 5 day and I
am not getting whether it is running properly or not. Could any one
kindly tell me how to see whether the simulation is running or not and
also how
Hello,
I know that is an already know problem but I don't know how to move on.
running pdb2gmx I had this message
Fatal error:
Atom CG is used in an interaction of type atom in the topology
database, but an atom of that name was not found in residue
number 163.
Residue 163 is a GLY and has no a
Hi ananya,
You can get the coordinates using trjconv:
trjconv -f file.xtc -s file.tpr -o file.pdb -b initial time in ps
-e final time in ps
this will give you pdb at the time you have mentioned.
For your first question- as far as I know you need to check whether
there is any periodic image
On 11/9/12 7:06 AM, Kavyashree M wrote:
Hi ananya,
You can get the coordinates using trjconv:
trjconv -f file.xtc -s file.tpr -o file.pdb -b initial time in ps
-e final time in ps
This is more easily accomplished with trjconv -dump. I would also advise making
a copy of the .trr/.xtc file
On 11/8/12 11:36 PM, tarak karmakar wrote:
Thanks Justin
As you see in the .mdp file I have used SHAKE. So if I want to fix
some C-C or C-O then what algorithm I have to use ?
It still doesn't make sense to me why you want to constrain only a subset of the
bonds in the system. Please
On 11/9/12 5:27 AM, Steven Neumann wrote:
Dear Gmx Users,
I used pdb2gmx to generate topology of the new molecule of which
parameters I added to ffbonded.itp and aminoacids.rtp creating new
resiude:
pdb2gmx -f LIG.pdb -o LIGproc.pdb -p topol.top
Back Off! I just backed up topol.top to
Hi,
On Tue, Nov 6, 2012 at 12:03 AM, Thomas Evangelidis teva...@gmail.comwrote:
Hi,
I get these two warnings when I run the dhfr/GPU/dhfr-solv-PME.bench
benchmark with the following command line:
mdrun_intel_cuda5 -v -s topol.tpr -testverlet
WARNING: Oversubscribing the available 0
On Fri, Nov 9, 2012 at 12:20 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/9/12 5:27 AM, Steven Neumann wrote:
Dear Gmx Users,
I used pdb2gmx to generate topology of the new molecule of which
parameters I added to ffbonded.itp and aminoacids.rtp creating new
resiude:
pdb2gmx -f LIG.pdb
After some investigation, it turns out that this is explained by the
differences in input radii for the GB-calculation done by Gromacs and Amber.
The radii in the gbsa.itp-file are not the same as the ones used by Amber.
If one changes the radii in gbsa.itp, you get a difference in 0-step
Hi, all,
Sometimes I do not need to dump the .trr file, which is really big.
I am wondering if I can avoid it?
Thank you very much.
Regards,
Kai
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Dear Gromacs Users,
I would like to study structure of a positively charged protein in the
vicinity of DNA. To do this, I want to perform replica exchange molecular
dynamics simulations in which DNA is frozen and only the protein moves.
This way I can efficiently obtain the free energy landscape
Dear Dejun:
I don't know why --enable-bluegene gives you problems or what it is supposed to
do. Was the BGQ even
available when gromacs 4.5.5 came out? I doubt it.
In any event, here is how my colleague successfully ran configure:
./configure \
--build=ppc64 \
By dumping, I presume you mean writing it to disk during mdrun.
set this in your .mdp file:
nstxout = 0
nstvout = 0
nstfout = 0
And, while you are at it:
nstlog = 0
Chris.
-- original message --
Sometimes I do not need to dump the .trr file, which is really big.
I am wondering if I can
Hi,
I would like to calculate the dipole moment (vector) of a functionality in
molecules, probably using g_dipoles. For example, suppose that my molecules
have hydroxyl functionalities; I would like to calculate the dipole moment
vectors of each hydroxyl group.
I can create an .ndx file with an
Hi again,
I forgot to mention that the functional groups that I will consider have
overall no net charge. I gave the hydroxyl group as a prototypical example
in my last post, but this is a bad example because hydroxyl groups are
typically not neutral. The groups that I will consider will be.
On 11/9/12 7:40 AM, Steven Neumann wrote:
On Fri, Nov 9, 2012 at 12:20 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/9/12 5:27 AM, Steven Neumann wrote:
Dear Gmx Users,
I used pdb2gmx to generate topology of the new molecule of which
parameters I added to ffbonded.itp and aminoacids.rtp
Dear All,
Reguarding a question I asked below. Does anyone know what the formulei,
etc...are for g_sham taking in 2 columns (or 3 with time) and turning it into a
density matrix. Is it just a count, summation on x-y or other?
Stephan Watkins
Original-Nachricht
Datum: Thu,
On Fri, Nov 9, 2012 at 3:29 PM, Christopher Neale
chris.ne...@mail.utoronto.ca wrote:
Dear Dejun:
I don't know why --enable-bluegene gives you problems or what it is
supposed to do. Was the BGQ even
available when gromacs 4.5.5 came out? I doubt it.
There's no code currently optimized for
On 11/9/12 9:02 AM, saber naderi wrote:
Dear Gromacs Users,
I would like to study structure of a positively charged protein in the
vicinity of DNA. To do this, I want to perform replica exchange molecular
dynamics simulations in which DNA is frozen and only the protein moves.
This way I can
On 11/9/12 1:02 PM, lloyd riggs wrote:
Dear All,
Reguarding a question I asked below. Does anyone know what the formulei,
etc...are for g_sham taking in 2 columns (or 3 with time) and turning it into a
density matrix. Is it just a count, summation on x-y or other?
Values are divided
Just to add to that -
The non-polar term of GBSA do not match between gmx and Amber11, presumably
due to different algorithms for computing the surface area.
I tried the different surface area options (gbsa keyword) in Amber11, but
it didn't help.
fyi.
Best
Sandeep
On Fri, Nov 9, 2012 at 8:32
Hi,
You must have an odd sysconf version! Could you please check what is the
sysconf system variable's name in the sysconf man page (man sysconf) where
it says something like:
_SC_NPROCESSORS_ONLN
The number of processors currently online.
The first line should be one of the
Hi,
can you suggest me how can i identify or specify the hydrophobic atoms to
the index files.
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Hi,
I see degrading scaling when going from 96 to 192 cores on a cray for my
system. I have periodic molecules and do umbrella sampling (with small
deviations from the reference) which might affect the performance. My code is
based on 4.5.5 without performance-critical modifications.
Erik
9
On 11/9/12 9:56 PM, Raj wrote:
Hi,
can you suggest me how can i identify or specify the hydrophobic atoms to
the index files.
One possible approach is to use a .tpr file to select by atom type. Otherwise a
combination of residue numbers and chosen atom names will create the correct
I second everything that Justin Lemkul wrote. This recent paper (C. A.
Brackley, M. E. Cates, and D. Marenduzzo, Phys. Rev. Lett. 109:168103 (2012))
have a few weak points in my opinion, but demonstrate the artifacts that arise
from freezing the DNA.
Best,
Erik
9 nov 2012 kl. 20.42 skrev
Hi,
Yes, e.g. by constructing elaborate virtual sites. The reason for doing so
remains unclear to me, however.
Best,
Erik
9 nov 2012 kl. 17.28 skrev afsaneh maleki:
Hi,
I am trying to simulate some organic molecules with gromacs. I want to
consider their internal structures of these
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