Dear Gromacs Users,
I want to study folding of isolated unstructured domain of the protein.
Do you have any recommendations which Force Field could possibly be used
for this purpose?
Thank you in advance.
Netaly Khazanov.
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Netaly
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Dear GROMACS users, I am using version 5.0.2.
I am studying the crystallization of a liquid molecular system, and I need to
study the Static Structure Factor for my system. I know that you can obtain
S(q)-1 setting the right option in g_rdf, but my questions are:
1) How does GROMACS compute it?
On 10/21/14 12:28 PM, Netaly Khazanov wrote:
Dear Gromacs Users,
I want to study folding of isolated unstructured domain of the protein.
Do you have any recommendations which Force Field could possibly be used
for this purpose?
Thank you in advance.
Netaly Khazanov.
You can start from this
Hi All,
I am pleased to announce that the CHARMM-GUI team has extended the capabilities
of CHARMM-GUI (www.charmm-gui.org) to provide GROMACS topologies, .mdp files,
and run scripts as part of the standard output of CHARMM-GUI. That is, one can
now assemble a system (even heterogeneous
With a time step of 0.0005 and still having the particle moved too far error,
I would suspect that your system is not well equilibrated. Likely you are going
to need to do some energy minimization and a short simulation with position
restraints to relax the system into equilibrium before doing
On 10/20/14 7:47 PM, Tom wrote:
Dear Gromacs Developer,
In the version of 5.0 or later, Gromacs has the functionalities
of Non-equilibrium MD by assigning the group of acceleration.
I am confused what is the difference between this acceleration
and the previous functionality of
On 10/20/14 8:57 PM, Jackson Chief Elk wrote:
Hello, I need to calculate the intermolecular interaction energy for water
confined to a micro cavity I simulated in a biphasic water-bromobutane
system. What I need to do is calculate the interaction energies ONLY for
water that is within 0.4nm
On 10/20/14 11:40 PM, lloyd riggs wrote:
Dear All,
So I have been doing membrane simulations on a small (really small) node for a
few months, and was able to get in a few hundred nanoseconds of time. I now
have added 4 inositol lipids, and repeatedly encounter some errors as follows.
I set
Thanks for the direction Justin. I will probably end up writing my own C
program that does this, possibly by using the system() function to call on
gromacs commands when needed. I'll be sure to put it on Sourceforge when its
done.
Cheers!
On Oct 21, 2014, at 6:28 AM, Justin Lemkul
Hi,
i am studied the capter 5 about topology, and o did not understand
some aspect:
1-in the a.tp file, what does means the number after the simbol?
0 15.999 (C==0)
OM 15.99 (CO)
C 12.01 (C=0, C-N)
2- witch differences are between O and C?
3- The file with the virtual sites what
Most of your questions are basic (bio)chemistry; I would suggest consulting some
textbook material before diving into simulations, which add another layer of
complexity.
On 10/21/14 12:30 PM, Marcello Cammarata wrote:
Hi,
i am studied the capter 5 about topology, and o did not understand
Hi there!
Does anyone know that how does the number of cpu cores and the clock speed
of each cpu core affects the GPU performance? Is there a sweetspot with
regards to performance?
Thanks a lot!
Jane
--
Dr. Jane Yin
Postdoctoral Researcher
3105 Gilson Lab Office
Skaggs School of Pharmacy and
Dear gmx users,
I am computing PCA on a system with 15476 atoms (a matrix of 46428x46428),
using g_covar. The covariance matrix seems to be built, however it crashes few
hours later after diagonalization takes place:
Calculating the average structure ...
trn version: GMX_trn_file (single
Dear GROMACS users
I received the following error while running grompp to prepare the .tpr
file before the initial energy minimization of my system.
*Fatal error:Group DNA_chain_D referenced in the .mdp file was not found in
the index file.Group names must match either [moleculetype] names
Dear all,I am intrigued by the error that I have received this morning, as follows:The charge group starting at atom 37920 moved more than the distance allowed by the domain decomposition (1.40) in direction Ydistance out of cell 7.144197Old coordinates: 54.499 39.697 14.058New coordinates:
Hi,
You should start by using a time step more appropriate to your use of
constraints = none, or vice versa.
Mark
On Wed, Oct 22, 2014 at 4:26 AM, Kester Wong kester2...@ibs.re.kr wrote:
Dear all,
I am intrigued by the error that I have received this morning, as follows:
The charge
On Wed, Oct 22, 2014 at 4:08 AM, Vinson Leung lwhvinson1...@gmail.com
wrote:
Hi all. I rencently I try different MPI library to run gromacs and find
that unlike Intel MPI and MPICH (which is normally can reach nearly 100%
CPU utilization ), it only can reach 20% CPU utilization when using
On Tue, Oct 21, 2014 at 11:46 PM, Mendez Giraldez, Raul
rmen...@email.unc.edu wrote:
Dear gmx users,
I am computing PCA on a system with 15476 atoms (a matrix of 46428x46428),
using g_covar. The covariance matrix seems to be built, however it crashes
few hours later after diagonalization
Hi Mark,Thanks for the input, I thought a time step of 2 fs is small enough?Should I change my constraint to constraints = h-bonds instead?Or,Should I use:dt = 0.001; 1 fsconstraints = noneconstraint-algorithm = shakeCheers,Kester
You should start by using a time step more appropriate to your
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