[gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 78
Mehreen Jan
mehreen_jan1990 at yahoo.com
Tue Feb 16 05:46:12 CET 2016
error:
the gmx executable was compiled to use the rdtscp CPU instruction. however this is not supported by the current hardware and continuing would ta a crash.please rebuild gromacs with GMX_USE_RTD SCP=OFF CMAKE option
is it is installation issue???
how to correct this issue???
any ides??
mehreen jan
--------------------------------------------
On Mon, 15/2/16, gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
Subject: gromacs.org_gmx-users Digest, Vol 142, Issue 78
To: gromacs.org_gmx-users at maillist.sys.kth.se
Received: Monday, 15 February, 2016, 10:14 PM
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Today's Topics:
1. Re: gromacs-5.1.1 installation error:
libxml2 problem
(Mark Abraham)
2. Shrink simulation box while maintaining
ensemble (Matthias Ernst)
3. Re: gromacs-5.1.1 installation error:
libxml2 problem
(Irina Kosheleva)
4. NVT-Eq ---> NVT-MD (Alexander
Alexander)
5. calculate *all* carbon atom distances
over time? (Athina Meletiou)
6. Re: NVT-Eq ---> NVT-MD (Justin
Lemkul)
7. Re: calculate *all* carbon atom
distances over time?
(Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Mon, 15 Feb 2016 15:29:32 +0000
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] gromacs-5.1.1 installation error:
libxml2
problem
Message-ID:
<CAMNuMASnQJKkO3-nTXaF3PNz75ohSy7g--t95Siywys4Ym2_cA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
Now that I have a computer again, I looked up what I did on
Vesta, and in
fact you don't need zlib support from libxml2, so just
configure libxml2
without that (and without python), and you'll be fine.
I am also looking at how we can take this useless activity
away from
people...
Mark
------------------------------
Message: 2
Date: Mon, 15 Feb 2016 16:35:40 +0100
From: Matthias Ernst <matthias.ernst at physik.uni-freiburg.de>
To: gmx-users at gromacs.org
Subject: [gmx-users] Shrink simulation box while maintaining
ensemble
Message-ID: <56C1F04C.90908 at physik.uni-freiburg.de>
Content-Type: text/plain; charset=utf-8
Hi,
I am running a protein folding simulation, starting with an
extended
structure that needs a lot of water molecules to fulfill the
minimial
image convenction.
Is there a way to "shrink" a simulation box and get rid of
unnecessary
solvent molecules while keeping velocities (to preserve the
ensemble as
far as possible and avoid re-equilibration)?
Thanks,
Matthias
--
Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611
------------------------------
Message: 3
Date: Mon, 15 Feb 2016 15:55:31 +0000
From: Irina Kosheleva <ikoshelev at cars.uchicago.edu>
To: "gmx-users at gromacs.org"
<gmx-users at gromacs.org>
Subject: Re: [gmx-users] gromacs-5.1.1 installation error:
libxml2
problem
Message-ID:
<F1EE0EEBA6FB8143A8387AB46F20E279650D8790 at CARSMAIL2.CARS.APS.ANL.GOV>
Content-Type: text/plain; charset="us-ascii"
Hi Mark,
Thank you for your suggestions
Indeed this works:
For libxml2:
./configure
--prefix=/home/ikosh/programs/autotools-bin
--without-python --without-zlib --without-lzma
cmake -DCMAKE_C_COMPILER=mpixlc_r
-DCMAKE_CXX_COMPILER=mpixlcxx_r
-DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C
-DGMX_SIMD=IBM_QPX
-DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF
-DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_C_FLAGS="-O3
-qsmp=omp -qarch=qp -qtune=qp"
-DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install
-- Looking for NVIDIA GPUs present in the system
-- Checking for MPI_IN_PLACE - yes
-- Looking for zlibVersion in
/home/ikosh/programs/autotools-bin/lib/libz.a
-- Looking for zlibVersion in
/home/ikosh/programs/autotools-bin/lib/libz.a - found
-- Found LibXml2:
/home/ikosh/programs/autotools-bin/lib/libxml2.a (found
version "2.9.3")
-- Looking for xmlTextWriterEndAttribute in
/home/ikosh/programs/autotools-bin/lib/libxml2.a
-- Looking for xmlTextWriterEndAttribute in
/home/ikosh/programs/autotools-bin/lib/libxml2.a -
found!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Irina.
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se]
On Behalf Of Mark Abraham
Sent: Monday, February 15, 2016 9:30 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] gromacs-5.1.1 installation error:
libxml2 problem
Hi,
Now that I have a computer again, I looked up what I did on
Vesta, and in
fact you don't need zlib support from libxml2, so just
configure libxml2
without that (and without python), and you'll be fine.
I am also looking at how we can take this useless activity
away from
people...
Mark
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
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or send a mail to gmx-users-request at gromacs.org.
------------------------------
Message: 4
Date: Mon, 15 Feb 2016 18:09:29 +0100
From: Alexander Alexander <alexanderwien2k at gmail.com>
To: gmx-users at gromacs.org
Subject: [gmx-users] NVT-Eq ---> NVT-MD
Message-ID:
<CAEDv6u7LOWJ2cps58VTFF1+ziEjS4dNHEuOQ6-eCdVU128Gn5A at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear Gromacs user,
I have an elementary question which I would be thankful if
one could
comment on it;
I want to do a NVT-MD simulation as a production calculation
of my MD
simulation for 10 ns, and suppose that a NVT- Equilibration
has been done
in advance for 0.5 ns. The normal differences between their
.mdp files are
coming below and the rest of their .mdp files are fully
identical;
NVT-Eq (Equilibration)
------------------------------------
nsteps = 500000 ; 0.5 ns
;Generate velocity
gen_vel = yes
gen_temp = 298.15
gen_seed = -1
-------------------------------------
NVT-MD (Production)
-------------------------------------
nsteps = 10000000 ; 10 ns
continuation = yes ;continuing from
NVT-Eq
;Generate velocity
gen_vel = no
-------------------------------------
Since they have identical .mdp parameters, then, my question
is that:
if it is possible to do just one NVT-MD simulation (a bit
longer (10 +
0.5)ns ) instead of two sequence NVT-Eq and NVT-MD
simulations?
Best regards,
Alex
------------------------------
Message: 5
Date: Mon, 15 Feb 2016 17:10:39 +0000
From: Athina Meletiou <enxam16 at nottingham.ac.uk>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] calculate *all* carbon atom distances
over time?
Message-ID:
<34F9D2746A2FF84AA4806F564A17E62601B2D9 at UIWEXMBX09.ad.nottingham.ac.uk>
Content-Type: text/plain; charset="us-ascii"
Hello all,
I was wondering how I could measure the distance over time
between all my carbon atoms in my simulation. My molecules
have interesting folding patterns and I would like to see
the distances between the unconnected carbon atoms as my
molecules fold and unfold through the simulation. My
simulations consist of single lipid molecules in water.
I have tried using g_dist but it seems that it's not what
I'm looking for as it calculates distances between groups of
atoms rather than individual atoms. Do you think that gmx
distance (Gromacs 5.0) will help me? What concerns me is
that in the gmx distance reference it states that "gmx
distance calculates distances between pairs of positions as
a function of time" - do the positions need to be in pairs,
as in always in even numbers?
Thank you all very much,
Athina
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------------------------------
Message: 6
Date: Mon, 15 Feb 2016 12:12:57 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] NVT-Eq ---> NVT-MD
Message-ID: <56C20719.7080103 at vt.edu>
Content-Type: text/plain; charset=windows-1252;
format=flowed
On 2/15/16 12:09 PM, Alexander Alexander wrote:
> Dear Gromacs user,
>
> I have an elementary question which I would be thankful
if one could
> comment on it;
>
> I want to do a NVT-MD simulation as a production
calculation of my MD
> simulation for 10 ns, and suppose that a NVT-
Equilibration has been done
> in advance for 0.5 ns. The normal differences between
their .mdp files are
> coming below and the rest of their .mdp files are fully
identical;
>
> NVT-Eq (Equilibration)
> ------------------------------------
> nsteps = 500000 ; 0.5 ns
>
> ;Generate velocity
> gen_vel = yes
> gen_temp = 298.15
> gen_seed = -1
> -------------------------------------
>
>
> NVT-MD (Production)
> -------------------------------------
> nsteps = 10000000 ; 10 ns
> continuation = yes ;continuing from
NVT-Eq
>
>
> ;Generate velocity
> gen_vel = no
> -------------------------------------
>
> Since they have identical .mdp parameters, then, my
question is that:
>
> if it is possible to do just one NVT-MD simulation (a
bit longer (10 +
> 0.5)ns ) instead of two sequence NVT-Eq and NVT-MD
simulations?
>
Of course. The normal use for separating two phases
(equilibration and
production) is in the case of restraints, shorter time step
for equilibration in
troublesome systems, etc. If you just have the same
settings, do a single run.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu
| (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 7
Date: Mon, 15 Feb 2016 12:14:32 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] calculate *all* carbon atom
distances over
time?
Message-ID: <56C20778.7080609 at vt.edu>
Content-Type: text/plain; charset=windows-1252;
format=flowed
On 2/15/16 12:10 PM, Athina Meletiou wrote:
> Hello all,
>
> I was wondering how I could measure the distance over
time between all my
> carbon atoms in my simulation. My molecules have
interesting folding patterns
> and I would like to see the distances between the
unconnected carbon atoms as
> my molecules fold and unfold through the simulation. My
simulations consist
> of single lipid molecules in water.
>
> I have tried using g_dist but it seems that it's not
what I'm looking for as
> it calculates distances between groups of atoms rather
than individual atoms.
A "group" can be one atom.
> Do you think that gmx distance (Gromacs 5.0) will help
me? What concerns me
> is that in the gmx distance reference it states that
"gmx distance calculates
> distances between pairs of positions as a function of
time" - do the
> positions need to be in pairs, as in always in even
numbers?
>
If you're looking at distances between any two atoms, why
would this be a concern?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu
| (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
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