Hi,
there is a question for hardware experts. What is the optimal hardware to
achieve better scalability in parallel MD simulations of 10K-100K atoms?
Probably, it should be a cluster of multi-cpu, multi-core units with fast
interconnection. In this case, what is the optimal=performance/price
con
On 4/28/10 9:38 AM, Igor Leontyev wrote:
Hi,
there is a question for hardware experts. What is the optimal hardware to
achieve better scalability in parallel MD simulations of 10K-100K atoms?
Probably, it should be a cluster of multi-cpu, multi-core units with fast
interconnection. In this case,
Hi gromacs users
about SA simulation, I saw in some papers that annealing _time is very
short. fpr example [The temperature was increased from 0 to 600 K over the
first 4 ps, held at 600 K for 2 ps, and then slowly cooled to 0 K over 14 ps
in simulation of protein-dna]. Is there limitation in ele
Hello,
On 27.04.2010, at 23:31, Nilesh Dhumal wrote:
> Hello,
> I am trying to plot radial distribution function between a atom and a
> center of two atoms.
> How can I calculate the centre of two atoms and further how can I use this
> center to plot radial distribution funciton?
>
you will ha
Michael McGovern wrote:
Hi everyone. I'm having some trouble using g_wham to analyze some
results. I have some simulations from gromacs 3.3 using the pull
code. I'm using the latest version of g_wham to analyze the results,
which the help file says is ok, using the -ip option.
I've gotten
I second Justin here, for Amber FF (which share essentially the same
topology but with different parameters with OPLS/AA), the impropers
dihedrals seems to be enough as for TRP.
Just a side note, using ACPYPE (which uses antechamber in the core) to
generate topologies for molecules like TRP, 6 ext
Hello Justin,
In my topology file I am declaring:
---
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Strong position restraints on rest of B2AR
#ifdef STRONG_
Anirban Ghosh wrote:
Hello Justin,
In my topology file I am declaring:
---
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Strong position restraints on re
shahid nayeem wrote:
Hi Justin
Should I try to do position restraint at 500k and then full MD simulation.
Always equilibrate under the conditions you wish to use prior to collecting data
under those conditions.
As for whether or not your force field is even valid at such high temperature i
shahab shariati wrote:
Hi gromacs users
about SA simulation, I saw in some papers that annealing _time is very
short. fpr example [The temperature was increased from 0 to 600 K over
the first 4 ps, held at 600 K for 2 ps, and then slowly cooled to 0 K
over 14 ps in simulation of protein-d
Dear All,
How is the 1-4 interaction treated when using Buckingham potential
for vdw type of interactions in gromacs?
As I understand from the manual one has to delete the [ pairs ]
section in the topology file (if present) and the
the scaling for 1-4 interaction will be 1.0.
Did I get it right?
Hi All,
I want to perform MD simulation of a protein in implicit solvent using
gromacs 4.0.7. I looked into the manual but did not get any information
regarding the implicit solvent. Is it avilable in gromacs? I searched in the
mailing list and found someone in older mail said its not avilable. I
Dear all,
With gromacs-4.0.5, one had the possibility to compile a 64-bit version of
gromacs for Mac OS X using configure --
enable-apple-64bit. This was even suggested by configure to improve performance.
With gromacs-4.0.7, the option --enable-apple-64bit of configure has
disappeared and confi
J. Rui Rodrigues wrote:
Dear all,
With gromacs-4.0.5, one had the possibility to compile a 64-bit version of
gromacs for Mac OS X using configure --
enable-apple-64bit. This was even suggested by configure to improve performance.
With gromacs-4.0.7, the option --enable-apple-64bit of configur
Chanchal wrote:
Hi All,
I want to perform MD simulation of a protein in implicit solvent using
gromacs 4.0.7. I looked into the manual but did not get any information
regarding the implicit solvent. Is it avilable in gromacs? I searched in
the mailing list and found someone in older mail s
>
> Michael McGovern wrote:
> > Hi everyone. I'm having some trouble using g_wham to analyze some
> > results. I have some simulations from gromacs 3.3 using the pull
> > code. I'm using the latest version of g_wham to analyze the results,
> > which the help file says is ok, using the -ip option
Implicit solvent are still not available in gromacs.
Using 43a1 FF is fine, except with implicit solvent! Or you should
have one compatible with it!
On Apr 28, 2010, at 6:27 PM, Chanchal wrote:
Hi All,
I want to perform MD simulation of a protein in implicit solvent
using gromacs 4.0.7. I
Hi,
So, there is something going wrong here...
My machine: Mac OS X 10.5.8 with 2 x 3.2 GHz Quad-Core Intel Xeon
--> Compilation of gromacs against fftw3 libs installed with fink (installed in
/sw/; no 64-bit libs) goes fine, but results in 32-bit binaries:
tar xvzf gromacs-4.0.7.tar.gz ; cd gr
Hi All,
I have some problems with g_wham, and i already gone through all the
postings and didn't find a hint..
basically, I'm trying to calculate PMF between two charged plates. I've
performed a pulling simulation between the 2 plates according to Justin's
UMBRELLA tutorial in the website (all st
Amir Marcovitz wrote:
Hi All,
I have some problems with g_wham, and i already gone through all the
postings and didn't find a hint..
For problems like these (which are hard to diagnose!), your Gromacs version,
compilers used, OS, etc. would be useful.
basically, I'm trying to calculate
Dear Gromacs Users
I have set my pull option as "constant force" and the pull geometry is
"distance"
the manual has stated that the pull_k1 unit is kJ/mol/nm . does it mean that
the force applied to the
protein is proportional to the distance between the 2 groups ? else what is
it ?
my second qu
Hello,
I am doing solvation of glucose. I am trying to calculate a angle between
three selected carbon atoms.
If I run g_angle using angle.ndx file it consider all carbon atom. In
force field C-C-C 112.5 is specified so its making a group of all carbon
atoms. I am interested in selected carbon ato
Nilesh Dhumal wrote:
Hello,
I am doing solvation of glucose. I am trying to calculate a angle between
three selected carbon atoms.
If I run g_angle using angle.ndx file it consider all carbon atom. In
force field C-C-C 112.5 is specified so it’s making a group of all carbon
atoms. I am interest
On 29/04/2010 5:22 AM, J. Rui Rodrigues wrote:
Hi,
So, there is something going wrong here...
My machine: Mac OS X 10.5.8 with 2 x 3.2 GHz Quad-Core Intel Xeon
--> Compilation of gromacs against fftw3 libs installed with fink (installed
in /sw/; no 64-bit libs) goes fine, but results in 32-b
Dear gmx experts,
I am having problem doing MD run for a hydrocarbon system. The system
contains a stack of Hexane molecules using editconf.
The distance between molecuels in the box is more than 30 A. I am wondering
why I get large forces (system is blowing up) with this distance!. (LINCS
warnin
Moeed wrote:
Dear gmx experts,
I am having problem doing MD run for a hydrocarbon system. The system
contains a stack of Hexane molecules using editconf.
The distance between molecuels in the box is more than 30 A. I am
wondering why I get large forces (system is blowing up) with this
di
Hello Justin,
Thanks a lot for your reply.
I am using the option "freezegrps" in my .mdp file, given below:
-
;define = -DSTRONG_POSRES
define
Hello Justin,
Thanks a lot for your reply.
I am using the option "freezegrps" in my .mdp file, given below:
-
;define = -DSTRONG_POSRES
define
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