Hi Roland:
Based on your test, how many speed-up you get?
Yorquant
2012/12/7 Roland Schulz
> On Thu, Dec 6, 2012 at 9:42 PM, Yorquant Wang wrote:
>
> > Hi Mark:
> > There is a new instruction set architecture (*Advanced Vector
> > Extensions
> > * (AVX)) that can make float calculation
On Thu, Dec 6, 2012 at 9:42 PM, Yorquant Wang wrote:
> Hi Mark:
> There is a new instruction set architecture (*Advanced Vector
> Extensions
> * (AVX)) that can make float calculation in Intel CPU faster two times
> compared with the old instruction set. I want to know if the Gromacs
> develo
On 12/6/12 9:42 PM, Yorquant Wang wrote:
Hi Mark:
There is a new instruction set architecture (*Advanced Vector Extensions
* (AVX)) that can make float calculation in Intel CPU faster two times
compared with the old instruction set. I want to know if the Gromacs
developers have a plan to m
Hi Mark:
There is a new instruction set architecture (*Advanced Vector Extensions
* (AVX)) that can make float calculation in Intel CPU faster two times
compared with the old instruction set. I want to know if the Gromacs
developers have a plan to make GMX support AVX. if the GMX can support GM
Dear Justin
Thank you for reply.
I added
#include "ffoplsaa.itp" into top and
#include "tip4p.itp"after [exclusions], as you told.
Then, I could make tpr file and MD looks working.
Thank you very much.
Kenji
- Original Message -
>> From: Justin Lemkul
>> To: Discussion list
On 12/6/12 8:22 PM, Nur Syafiqah Abdul Ghani wrote:
Dear Users,
May I know after do the command
genbox -cp prot_box.gro -ci solvent.gro -nmol 2000 -cs spc216.gro -p
control.top -o prot_mix_sol.gro
the result shows,
Output configuration contains 1121788 atoms in 367835 residues
Volume
Am 06.12.2012 21:16, schrieb Justin Lemkul:
>
>
> On 12/6/12 3:12 PM, fatemeh ramezani wrote:
>> hello
>> I want to simulate gold nanoparticles with proteins. I've made a
>> PDF file containing the nanoparticles and proteins, using Hayprkm
>> software.then Ihave used thisPDF fileto start the simu
On 12/6/12 3:12 PM, fatemeh ramezani wrote:
hello
I want to simulate gold nanoparticles with proteins. I've made a PDF file
containing the nanoparticles and proteins, using Hayprkm software.then Ihave
used thisPDF fileto start the simulation by gromacs. But in the early stage of
equilibriu
hello
I want to simulate gold nanoparticles with proteins. I've made a PDF file
containing the nanoparticles and proteins, using Hayprkm software.then Ihave
used thisPDF fileto start the simulation by gromacs. But in the early stage of
equilibrium, I am faced with the following error.
applica
They have also the complete force field parameters under:
OPLS Auxiliary topologyoplsaaff.itp
if there are more paramters then in the oplsaa.ff directiory, then they
have probably developed these parameters.
They give this paper as a reference for the calculations. Probably
something is
Justin,
Thanks again for explanation.
It's interesting that above parametrization made by ATB have cased the
system to crash within first ps of modeling ;) (On the contrarythe
system with the ligand made by prodrg have been very stable during
100ns). I ve tried to re-parametrized my molecule by
Dear users, I have a question concerning g_analyze:
I have N similar time-dependent datasets, calculate autocorrelation
functions using "g_analyze -f -ac -n -nosubav" and get N results. I
found that the program can also be called with the option -oneacf, but
was not able yet to find out, what thi
Dear Tomas,
Thanks for your information!
I look at the website you mentioned:
http://virtualchemistry.org/molecules/110-02-1/index.php
The *top file is available and the atom opls-aa types are assigned on *top
file.
But I can not find these parameters of dihedral angles from the default gmx
(VERS
Okay. Thanks for the fix, it worked.
Hubert
2012/12/6 Roland Schulz
> Hi,
>
>
> On Thu, Dec 6, 2012 at 4:58 AM, hubert santuz >wrote:
>
> >
> > The building/compilation of gromacs itself is working.
> > But, when I try to compile the template file to create my own plugin, it
> > fails.
>
>
> Y
On 12/6/12 5:46 AM, Kavyashree M wrote:
Sir,
I also have come across several papers where they have done
single simulations but in recent days most of them perform
multiple trajectories for shorter period. But I am not clear how
can multiple trajectories for shorter period of time compensate
f
On 12/6/12 6:09 AM, Kenji Mochizuki wrote:
Dear GMX users
Could you tell me how to make the topology file for ammonia in tip4p water?
I made topology file for ammonia by hand, as shown at end.
MD dose work when system has only ammonia molecules.
For ammonia in water,
I had though it needed t
On 12/6/12 5:26 AM, Erik Marklund wrote:
5 dec 2012 kl. 17.26 skrev Justin Lemkul:
On 12/5/12 11:21 AM, Kavyashree M wrote:
Sir,
Thank you for your suggestions. I decided the cutoff based on
RMSD convergence. I will calculate at different time intervals.
Running multiple simulation is de
On 12/6/12 2:39 AM, James Starlight wrote:
Justin,
Could you provide me with the example of the server where I could
obtain Gromac's itp topologies for the charmm ff? I know many such
servers which could be useful only for preparation systems for NAMD
program.
Google "CHARMM ligand topology
On 12/6/12 7:06 AM, venkatesh s wrote:
Respected gromacs people's,
for protein and ligand complex i want use opls ff, here found mktop for
ligand (external tool in gromacs web-page) but it only provide topology
file only,my question is were i will get the .gro file and .itp file ?
If the pro
Respected gromacs people's,
for protein and ligand complex i want use opls ff, here found mktop for
ligand (external tool in gromacs web-page) but it only provide topology
file only,my question is were i will get the .gro file and .itp file ?
Thank You
--
Regards,*
*S.VENKATESH,
--
gmx-users ma
Hi,
On Thu, Dec 6, 2012 at 4:58 AM, hubert santuz wrote:
>
> The building/compilation of gromacs itself is working.
> But, when I try to compile the template file to create my own plugin, it
> fails.
Yes. I broke that for beta1. If you don't want to wait for beta2 or 3 (not
sure it'll make it
Dear GMX users
Could you tell me how to make the topology file for ammonia in tip4p water?
I made topology file for ammonia by hand, as shown at end.
MD dose work when system has only ammonia molecules.
For ammonia in water,
I had though it needed to add just two line at the top of .top file.
Have a look there:
http://virtualchemistry.org/molecules/110-02-1/index.php
"virtualchemistry.org" is a really nice site (from David van der Spoel,
and others i think), which has many paramters for solvents for the GAFF
and OPLS force field. And also Physical properties for these.
Greetings
T
Sir,
I also have come across several papers where they have done
single simulations but in recent days most of them perform
multiple trajectories for shorter period. But I am not clear how
can multiple trajectories for shorter period of time compensate
for single extended time simulation.
Thank y
5 dec 2012 kl. 17.26 skrev Justin Lemkul:
>
>
> On 12/5/12 11:21 AM, Kavyashree M wrote:
>> Sir,
>>
>> Thank you for your suggestions. I decided the cutoff based on
>> RMSD convergence. I will calculate at different time intervals.
>> Running multiple simulation is definitely the best suggesti
Hi everyone,
First, here my system :
Ubuntu 12.04 64 bits
gcc : 4.6.3
cmake : 2.8.7
fftw : 3.3.3 including SSE 2
The building/compilation of gromacs itself is working.
But, when I try to compile the template file to create my own plugin, it
fails.
First, I'm sourcing Gromacs.
The building pa
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