I hoped that the package (gromacs_win32.zip,
http://www.gromacs.org/Downloads/User_contributions/Gromacs_binaries/i686%2f%2fMS_Windows
), with programs, which are ready to execution, will accelerate my time of
study of the GROMACS program, but it appeared that I got stuck on a step
GROMPP.
There w
On 2/27/15 10:21 AM, Vasiliy Znamenskiy wrote:
I hoped that the package (gromacs_win32.zip,
http://www.gromacs.org/Downloads/User_contributions/Gromacs_binaries/i686%2f%2fMS_Windows
), with programs, which are ready to execution, will accelerate my time of
study of the GROMACS program, but it ap
On 2/27/15 6:07 AM, Seera Suryanarayana wrote:
Dear gromacs users
I would like to calculate the free energy of simulated protein, how does it
can be done?
Surya
Graduate student
India.
Free energy with respect to what? There is no absolute free energy.
m.
--
Gromacs Users mailing list
* Plea
Szilárd thank you for the useful adivices about the configuration of the new
server machine.
I report the changes made to improve the performance of a molecular dynamics
on a protein of 1925 running on GPU INVIDIA K20 Tesla :
a.. To limit the number of cores used in the calculation (optio
Szilárd thank you for the useful adivices about the configuration of the new
server machine.
I report the changes made to improve the performance of a molecular dynamics
on a protein of 1925 running on GPU INVIDIA K20 Tesla :
a.. To limit the number of cores used in the calculation (optio
I report the changes made to improve the performance of a molecular dynamics
on a protein of 1925 running on GPU INVIDIA K20 Tesla :
a.. To limit the number of cores used in the calculation (option -pin on)
and to have a better performance:
"gmx_mpi mdrun ... -ntomp 16 -pin on"
where ntomp i
Hello GROMACS users,
I have a problem with the Replica Exchange statistics printed in log file.
I ran a 25 ns Replica exchange on a cluster through a queuing system.
However, due to insufficient wall time the job stopped abruptly around 24
ns and no stats were printed in the log file. I then exten
Dear All,
I would like to statically compile GROMACS 5 in an Intel Xeon X3430 machine
with gcc4.7 (cluster front node) BUT run it on an Intel Xeon E5-2650V2
machine (cluster compute node).
Would that be possible ? And if so, how should I do it ?
Haven't found it on the Installation_Instructions
Hi,
Thank you all for your anwsers.
Let me explain the circumstances that sorround this. I'm using a
developer's version of ACEMD, which grant me access to its internal data
structures.
When I run this version of acemd, it gives me the information of all the
atoms, bonds, angles, dihedrals, exclus
You need to cross-compile by selecting the SIMD support and possibly
RDTSCP support. It's here:
http://www.gromacs.org/Documentation/Installation_Instructions#portability-aspects
--
Szilárd
On Fri, Feb 27, 2015 at 2:54 PM, David McGiven wrote:
> Dear All,
>
> I would like to statically compile G
Woop! Sorry. I didn't see it before. Thanks.
2015-02-27 15:10 GMT+01:00 Szilárd Páll :
> You need to cross-compile by selecting the SIMD support and possibly
> RDTSCP support. It's here:
>
> http://www.gromacs.org/Documentation/Installation_Instructions#portability-aspects
> --
> Szilárd
>
>
> On
Dear Users
My problem is solved and GROMACS is running successfully on multiple nodes
now. The problem was that I accidentally modified a ".ssh" file in such a
way that it broke the system's ability to spread the job among cluster
nodes.
This was fixed by my system administrator.
Thanks & Regards
The original of this message was sent on 2/18. To date it has greeted
freeted with thundering silence. I would really appreciate an answer,
even if no solution is readily apparent.
I have compiled and installed Gromacs v-5.0.4 (rather than using the
version bundled with the distribution() in
On 2/26/15 5:39 PM, Thomas Lipscomb wrote:
Dear gmx-users,
Ok I understand. My specific question is how do I do these two tasks:
1. What do I need to change about the KALP15 with DPPC tutorial (again
substituting maximin 3 for KALP15) so that when I repeat it I get better data,
because some
Hi,
I'll be more direct this time. What potential shifts are the other software
packages using? GROMACS uses one by default.
Mark
On Fri, Feb 27, 2015 at 3:06 PM, IÑIGO SAENZ <
inigo.saen...@estudiant.upf.edu> wrote:
> Hi,
>
> Thank you all for your anwsers.
> Let me explain the circumstances t
On 2/26/15 10:25 PM, Aarti rana wrote:
I tried the same on a single frame also. It's been 24 hrs and still showing
running :
A single frame should be done in about a second. If it's hanging for any longer
than that, something is wrong. Either the binary fails (try running DSSP
directly,
On Fri, Feb 27, 2015 at 12:07 PM, Abhi Acharya
wrote:
> Hello GROMACS users,
>
> I have a problem with the Replica Exchange statistics printed in log file.
> I ran a 25 ns Replica exchange on a cluster through a queuing system.
> However, due to insufficient wall time the job stopped abruptly aro
On Fri, Feb 27, 2015 at 7:16 AM, Man Hoang Viet wrote:
> Dear GROMACS team,
>
> I am looking for source code of the old version (v1.0 to v2.0) of GROMACS,
> which is not available for downloading on GROMACS home page.
> Could you please share them to me?
>
I didn't find them on the ftp server in
On 2/27/15 2:00 AM, soumadwip ghosh wrote:
Dear users,
I have a query about some reviews one a paper which I
submitted recently. It deals with the binding of molecular ions with double
stranded DNA segments. My questions are-
1. Is it customary to take into account The centr
Good to hear! However, are you sure the "Number of CPUs detected (16)
does not match the number reported by OpenMP (1)" message was also
solved by the same? You should try to make this go away by telling
your MPI what threads/rank count you want, otherwise you *may*
experience performance loss.
--
On 2/27/15 4:01 PM, Stephen P. Molnar wrote:
The original of this message was sent on 2/18. To date it has greeted freeted
with thundering silence. I would really appreciate an answer, even if no
solution is readily apparent.
I have compiled and installed Gromacs v-5.0.4 (rather than using
The following problem is still there :
Number of CPUs detected (16) does not match the number reported by OpenMP
(1).
Consider setting the launch configuration manually!
The above message is always there and I am not sure about how to set it.
Even when I set OpenMP threads manually it shows.
I ra
Hi Dear Gromacs Users
I am following umbrella sampling tutorial provided by Dr Justin Lemkul
(This tutorial is not updated for Gromacs 5 However I am using Gromacs
5.0.2 and i am trying my best to use files and commands compatible with
version 5)
I have done all the parts up to pulling section ver
Excuse me that I forgot to attach the complete Error page:
nima@nima-ThinkPad:~/Desktop/3$ gmx grompp -f md_pull.mdp -c npt.gro -p
topol.top -n index.ndx -t npt.cpy -o pull.tpr
GROMACS:gmx grompp, VERSION 5.0.2
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen
Hi,
Did you check the parameters in .mdp file for pulling simulation?!
I think you have to define this pulling group in .mdp file that you use in
grompp.
On Fri, Feb 27, 2015 at 7:16 PM, Nima Soltani wrote:
> Excuse me that I forgot to attach the complete Error page:
> nima@nima-ThinkPad:~/Des
Thank you for your reply.
Stephen P. Molnar, Ph.D.Life is a fuzzy
set
Foundation for Chemistry Stochastic and
multivariate
www.FoundationForChemistry.com
(614)312-7528 (c)
Skype: smolnar1
-Original Message-
From: groma
On 2/27/15 7:16 PM, Nima Soltani wrote:
Excuse me that I forgot to attach the complete Error page:
nima@nima-ThinkPad:~/Desktop/3$ gmx grompp -f md_pull.mdp -c npt.gro -p
topol.top -n index.ndx -t npt.cpy -o pull.tpr
GROMACS:gmx grompp, VERSION 5.0.2
GROMACS is written by:
Emile Apol
Dear Users
My system can be identified into 2 groups ( default ) namely DNA and
Protein. To use the pull code , I want to apply pulling force on DNA and
keep Protein fixed.
Now, I have two itp files for my protein ( two chains,A and B). So do I
need to include something like this :-
; Include Pos
On 2/27/15 8:28 PM, Agnivo Gosai wrote:
Dear Users
My system can be identified into 2 groups ( default ) namely DNA and
Protein. To use the pull code , I want to apply pulling force on DNA and
keep Protein fixed.
Now, I have two itp files for my protein ( two chains,A and B). So do I
need to
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