from:"Sergio Manzetti"

Re: [gmx-users] where can I download POPC membrane file?

2011-05-29 Thread Sergio Manzetti

You can build it using VMD (VIsual Molecular Dynamics)



2011/5/30 albert 

> Dear all:
>
>   I would like to use charmm36 and POPC for membrane protein simulation.
> and I am wondering where can I download charmm36 pre-pribriumed POPC PDB and
> topol file for gromacs?
>
> Thank you very much
> Best
>
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Re: [gmx-users] RE: Metal surfaces (Sergio Manzetti)

2011-04-28 Thread Sergio Manzetti

Thank you

On Thu, Apr 28, 2011 at 6:26 PM, Ran Friedman  wrote:

> Hi,
>
> That's unlikely, but maybe the following publications can help you to build
> the surface:
>
>
> @Article{Iori2008,
> author = "Iori, F and Corni, S",
> title = {Including image charge effects in the molecular dynamics
> simulations of molecules on metal surfaces},
> journal = "J Comput Chem",
> year = "2008",
> volume = "29",
> pages = "1656-1666"
> }
>
> @Article{Iori2009,
> author = "Iori, F and Di Felice, R and Molinari, E and Corni, S",
> title = {{G}ol{P}: {A}n atomistic force-field to describe the interaction
> of proteins with {A}u(111) surfaces in water},
> journal = "J Comput Chem",
> year = "2009",
> volume = "30",
> pages = "1465-1476"
> }
>
> @article{Kalcher2009,
> Author = {Kalcher, I. and Horinek, D. and Netz, R. R. and Dzubiella, J.},
> Title = {{Ion specific correlations in bulk and at biointerfaces}},
> Journal = {JOURNAL OF PHYSICS-CONDENSED MATTER},
> Year = {{2009}},
> Volume = {{21}},
> Article-Number = {{424108}}
> }
>
> 
> Ran Friedman
> Biträdande Lektor (Assistant Professor)
>
> Linnaeus University
> School of Natural Sciences
> 391 82 Kalmar, Sweden
>
> Norrgård, room 328d
> +46 480 446 290 Telephone
> +46 76 207 8763 Mobile
> ran.fried...@lnu.se
> http://lnu.se/ccbg
> 
>
> Hello, does anybody have an idea if there are availbale PDB files which
> represent metal surfaces for transition state metals, to be used for MD?
>
> BW
>
> S
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[gmx-users] Metal surfaces

2011-04-28 Thread Sergio Manzetti

Hello, does anybody have an idea if there are availbale PDB files which
represent metal surfaces for transition state metals, to be used for MD?

BW

S
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Re: [gmx-users] Citation for NICS

2011-03-25 Thread Sergio Manzetti

Beacuse I want to cite NICS.

On Fri, Mar 25, 2011 at 8:56 PM, Emanuel Peter <
emanuel.pe...@chemie.uni-regensburg.de> wrote:

> Hello,
>
> Why do you ask this ?
>
>
>
> >>> Sergio Manzetti 25.03.11 13.09 Uhr >>>
>
> Hello everyone, is this citation proper for citing NICS?
>
> I.I. Rabi, J.R. Zacharias, S. Millman, P. Kusch (1938). "A New Method of
> Measuring Nuclear Magnetic Moment". *Physical 
> Review<http://en.wikipedia.org/wiki/Physical_Review>
> * *53*: 318. doi <http://en.wikipedia.org/wiki/Digital_object_identifier>:
> 10.1103/PhysRev.53.318 <http://dx.doi.org/10.1103%2FPhysRev.53.318>. 
> PMID<http://en.wikipedia.org/wiki/PubMed_Identifier>
>  9981980 <http://www.ncbi.nlm.nih.gov/pubmed/9981980>.
>
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[gmx-users] Citation for NICS

2011-03-25 Thread Sergio Manzetti

Hello everyone, is this citation proper for citing NICS?

I.I. Rabi, J.R. Zacharias, S. Millman, P. Kusch (1938). "A New Method of
Measuring Nuclear Magnetic Moment". *Physical
Review
* *53*: 318. doi :
10.1103/PhysRev.53.318 .
PMID
 9981980 .
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[gmx-users] g_RMS: Mismatch of atom number between topology and reference structure

2011-03-07 Thread Sergio Manzetti

Hello, I am doing a refolding experiment, but I re-experience the same
error. First of all, I use pdb2gmx for an input PDB structure, choose
OPLS/AA force field and vacuum settings (no waters).

Then I amke a box, and start simulations.

What I want to do is to compare the starting unfolded structure of the
simulation and its changes during the sim (all represented as a traj.xtc) to
a native folded conformation of the structure. Assuming it to be possible, I
thought of using g_rms;

g_rms -f native-folded.gro -s topol.tpr


Then I get the same error message:

WARNING: topology has 497 atoms, whereas trajectory has 491

---
Program g_rms, VERSION 4.5.1
Source code file: mshift.c, line: 102

Fatal error:
Molecule in topology has atom numbers below and above natoms (491).

Thing is that both the topology and the trajectory are treated equally at
the pdb2gmx step. So how can it be?

Sergio
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Re: [gmx-users] GAUSSIAN Error message

2011-02-24 Thread Sergio Manzetti

No. It contains a charged Gandolinium ion in the middle of a buckyball.



On Fri, Feb 25, 2011 at 2:59 AM, TJ Mustard  wrote:

>
> On February 24, 2011 at 10:29 AM Sergio Manzetti <
> sergio.manze...@vestforsk.no> wrote:
>
>  Hello, I am getting an unknown error message in the submission of the G03
> file:
>
>   QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.
>  # HF/6-31G OPT FREQ ^M ^M ARGUSLAB-GENERAT
>  '
>  Last state="GCL"
>  TCursr=  909 LCursr=   20
>  Error termination via Lnk1e in Gaussian64/g03/l1.exe at Thu Feb 24
> 19:26:31 2011.
>  Job cpu time:  0 days  0 hours  0 minutes  0.1 seconds.
>  File lengths (MBytes):  RWF=  9 Int=  0 D2E=  0 Chk=  1
> Scr=  1
>
>
> The submission file is prepared in Argus Lab and looks as follows:
>
> %chk=BuckyBall.chk
> # HF/6-31G Opt Freq
>
> ArgusLab-generated input file for BuckyBall
>
>  0  3
>
>
>  You have a no charge triplet? Is this a carbene?
>
>
>
>
> TJ Mustard
>
> C-0.677394-0.928398-3.166238 C0.672998-0.928446
> -3.166308
> C1.0902870.355662-3.166349
> C-0.0022521.149252-3.166236
> C-1.0947610.355692-3.166308
> C-2.2073000.717126-2.443529
> C-1.364869-1.874482-2.443334
> C1.360544-1.874612-2.443455
> C2.2027690.717064-2.443539
> C-0.0022732.318671-2.443310
> C2.453119-1.519766-1.733636
> C2.878066-0.212169-1.733664
> C2.2026961.865587-1.733573
> C1.0901852.673574-1.733478
> C-1.0947502.673602-1.733477
> C-2.2072941.865663-1.733587
> C-2.882593-0.212075-1.733651
> C-2.457472-1.519622-1.733552
> C-0.689644-2.803573-1.733436
> C0.685341-2.803673-1.733490
> C-1.364814-3.022879-0.584899
> C-2.457440-2.229447-0.584919
> C1.360538-3.023080-0.584938
> C2.453142-2.229641-0.584965
> C3.2954420.362133-0.584991
> C2.8779911.646286-0.584972
> C0.6728813.247762-0.584900
> C-0.6774413.247772-0.584900
> C-2.8826691.646412-0.584987
> C-3.3001250.362235-0.584997
> C-0.677324-3.2462440.584596
> C0.673012-3.2463560.584600
> C2.878165-1.6449290.584675
> C3.295525-0.3607300.584685
> C2.4530282.2310400.584637
> C1.3604223.0245220.584617
> C-2.4576442.2311330.584645
> C-1.3649783.0245500.584620
> C-2.882566-1.6447980.584681
> C-3.300136-0.3606380.584699
> C1.090333-2.6722231.733208
> C2.202882-1.8642451.733311
> C-2.207252-1.8641231.733266
> C-1.094677-2.6721151.733166
> C-2.8827100.2136741.733376
> C-2.4576671.5212871.733309
> C-0.6897782.8052321.733169
> C0.6852562.8052261.733176
> C2.8781580.2135981.733360
> C2.4531091.5212171.733301
> C-0.002190-2.3172212.442969
> C-2.207307-0.7155702.443173
> C-1.3649941.8761052.443040
> C1.3604901.8760862.443059
> C2.202875-0.7156462.443217
> C-0.6774280.9299253.165780
> C0.6729580.9299153.165806
> C1.090307-0.3541913.165883
> C-0.002209-1.1477443.165767
> C-1.094738-0.3541563.165831
> Gd-0.0048700.001706-0.000166
>
> --Link1--
> %chk=BuckyBall.chk
> # HF/6-31G Opt FreqCube=(orbitals)
>  Geom=AllCheck Guess=(Read,Only)
>
> BuckyBall_orbitals.cub
>   212   213
>
> --Link1--
> %chk=BuckyBall.chk
> # HF/6-31G Opt FreqCube=(density)
>  Geom=AllCheck Guess=(Read,Only)
>
> BuckyBall_density.cub
>
> --Link1--
> %chk=BuckyBall.chk
> # HF/6-31G Opt FreqCube=(spin)
>  Geom=AllCheck Guess=(Read,Only)
>
> BuckyBall_spin.cub
>
> --Link1--
> %chk=BuckyBall.chk
> # HF/6-31G Opt FreqCube=(potential)
>  Geom=AllCheck Guess=(Read,Only)
>
> BuckyBall_potential.cub
>
>
>
>
>
> TJ Mustard
> Email: musta...@onid.orst.edu
>
> --
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[gmx-users] GAUSSIAN Error message

2011-02-24 Thread Sergio Manzetti

Hello, I am getting an unknown error message in the submission of the G03
file:

  QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.
 # HF/6-31G OPT FREQ ^M ^M ARGUSLAB-GENERAT
 '
 Last state="GCL"
 TCursr=  909 LCursr=   20
 Error termination via Lnk1e in Gaussian64/g03/l1.exe at Thu Feb 24 19:26:31
2011.
 Job cpu time:  0 days  0 hours  0 minutes  0.1 seconds.
 File lengths (MBytes):  RWF=  9 Int=  0 D2E=  0 Chk=  1
Scr=  1


The submission file is prepared in Argus Lab and looks as follows:

%chk=BuckyBall.chk
# HF/6-31G Opt Freq

ArgusLab-generated input file for BuckyBall

 0  3
C-0.677394-0.928398-3.166238
C0.672998-0.928446-3.166308
C1.0902870.355662-3.166349
C-0.0022521.149252-3.166236
C-1.0947610.355692-3.166308
C-2.2073000.717126-2.443529
C-1.364869-1.874482-2.443334
C1.360544-1.874612-2.443455
C2.2027690.717064-2.443539
C-0.0022732.318671-2.443310
C2.453119-1.519766-1.733636
C2.878066-0.212169-1.733664
C2.2026961.865587-1.733573
C1.0901852.673574-1.733478
C-1.0947502.673602-1.733477
C-2.2072941.865663-1.733587
C-2.882593-0.212075-1.733651
C-2.457472-1.519622-1.733552
C-0.689644-2.803573-1.733436
C0.685341-2.803673-1.733490
C-1.364814-3.022879-0.584899
C-2.457440-2.229447-0.584919
C1.360538-3.023080-0.584938
C2.453142-2.229641-0.584965
C3.2954420.362133-0.584991
C2.8779911.646286-0.584972
C0.6728813.247762-0.584900
C-0.6774413.247772-0.584900
C-2.8826691.646412-0.584987
C-3.3001250.362235-0.584997
C-0.677324-3.2462440.584596
C0.673012-3.2463560.584600
C2.878165-1.6449290.584675
C3.295525-0.3607300.584685
C2.4530282.2310400.584637
C1.3604223.0245220.584617
C-2.4576442.2311330.584645
C-1.3649783.0245500.584620
C-2.882566-1.6447980.584681
C-3.300136-0.3606380.584699
C1.090333-2.6722231.733208
C2.202882-1.8642451.733311
C-2.207252-1.8641231.733266
C-1.094677-2.6721151.733166
C-2.8827100.2136741.733376
C-2.4576671.5212871.733309
C-0.6897782.8052321.733169
C0.6852562.8052261.733176
C2.8781580.2135981.733360
C2.4531091.5212171.733301
C-0.002190-2.3172212.442969
C-2.207307-0.7155702.443173
C-1.3649941.8761052.443040
C1.3604901.8760862.443059
C2.202875-0.7156462.443217
C-0.6774280.9299253.165780
C0.6729580.9299153.165806
C1.090307-0.3541913.165883
C-0.002209-1.1477443.165767
C-1.094738-0.3541563.165831
Gd-0.0048700.001706-0.000166

--Link1--
%chk=BuckyBall.chk
# HF/6-31G Opt FreqCube=(orbitals)
 Geom=AllCheck Guess=(Read,Only)

BuckyBall_orbitals.cub
  212   213

--Link1--
%chk=BuckyBall.chk
# HF/6-31G Opt FreqCube=(density)
 Geom=AllCheck Guess=(Read,Only)

BuckyBall_density.cub

--Link1--
%chk=BuckyBall.chk
# HF/6-31G Opt FreqCube=(spin)
 Geom=AllCheck Guess=(Read,Only)

BuckyBall_spin.cub

--Link1--
%chk=BuckyBall.chk
# HF/6-31G Opt FreqCube=(potential)
 Geom=AllCheck Guess=(Read,Only)

BuckyBall_potential.cub
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[gmx-users] Radial distribution function in gromacs

2011-01-26 Thread Sergio Manzetti

Hello every1,
I have a question about interpretation of g_rdf.

I have generated a plot with g_rdf (with -com flag) of a nanoparticle in
water, and it shows an unstable graph (y-axis) the first picoseconds , and
then a smoothing of the curve towards the zero the more r-value on the
x-axis increases. I chose the solvent as a reference group, and the
nanoparticle as a group.

Does this mean that the nanoparticle reaches a stable radial distribution
and thereby converges to a stable ensemble in water?

Best wishes

Sergio
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[gmx-users] Fwd: Viewing results from Groamcs QM/MM sims

2011-01-20 Thread Sergio Manzetti

Hi everyone,


Does anyone have a suggestion for a free program to view QM/MM results from
Gromacs?

Thanks

"The HiJacker"

a.ka. S
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[gmx-users] QM/MM viewer

2011-01-20 Thread Sergio Manzetti

Does anyone know of a free-of-charge viewer for QM/MM results from G03, for
Ubuntu? It should be able to show electron orbitals, polarizabilities, bond
strength etc.

Sergio
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[gmx-users] Mesa GLproto stuff UBUNTU

2011-01-20 Thread Sergio Manzetti

Hello, I am wondering if anyone has had luck installing glproto for a
functional Mesa package on Ubuntu? Thing is I am trying to install
wxmacmolplt-7.4.2 to view QM/MM results, but get nowhere without a
functional Open GL emulator.

Thanks

Sergio
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Re: [gmx-users] Ubuntu Installation

2011-01-11 Thread Sergio Manzetti

Thanks, doing # sudo apt-get install libfftw3-dev fixed the problem

Sergio

On Tue, Jan 11, 2011 at 7:31 AM, Jussi Lehtola wrote:

> On Tue, 11 Jan 2011 07:00:46 -0600
> Sergio Manzetti  wrote:
>
> > Dear users, I have installed FFTW3 successfully, and confirmed its
> > location using locate:
> >
> >
> > However, when I try installing Gromacs 4.5.3 the -/configure step
> > yields:
> >
> > configure: error: Cannot find fftw3f library
> >
> >
> > What am I doing incorrectly?
>
> Looks like you're missing the development package. Run
>
> # apt-get install libfftw3-dev
>
> to fix this.
> --
> --
> Mr. Jussi Lehtola, M. Sc., Doctoral Student
> Department of Physics, University of Helsinki, Finland
> jussi.leht...@helsinki.fi
> --
> Jussi Lehtola, FM, Tohtorikoulutettava
> Fysiikan laitos, Helsingin Yliopisto
> jussi.leht...@helsinki.fi, p. 191 50632
> --
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Ubuntu Installation

2011-01-11 Thread Sergio Manzetti

Thanks,

so  LDFLAGS /home/user/gmx
and CPPFLAGS /home/user/gmx  for example?

On Tue, Jan 11, 2011 at 2:19 PM, Justin A. Lemkul  wrote:

>
>
> Sergio Manzetti wrote:
>
>> Hi Justin, it was a blank ./configure
>>
>>
>>
> I don't know why a standard location like /usr/lib isn't be detected as
> containing the libraries, but you can set LDFLAGS and CPPFLAGS accordingly
> so that the libraries and headers are found.  See the installation
> instructions for details.
>
> -Justin
>
>
>> On Tue, Jan 11, 2011 at 2:03 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Sergio Manzetti wrote:
>>
>>Dear users, I have installed FFTW3 successfully, and confirmed
>>its location using locate:
>>
>>
>>/home/m/Desktop/gromacs-4.5.3/src/mdlib/gmx_fft_fftw3.c
>>/usr/lib/libfftw3.so.3
>>/usr/lib/libfftw3.so.3.2.4
>>/usr/lib/libfftw3_threads.so.3
>>/usr/lib/libfftw3_threads.so.3.2.4
>>/usr/lib/libfftw3f.so.3
>>/usr/lib/libfftw3f.so.3.2.4
>>/usr/lib/libfftw3f_threads.so.3
>>/usr/lib/libfftw3f_threads.so.3.2.4
>>/usr/lib/libfftw3l.so.3
>>/usr/lib/libfftw3l.so.3.2.4
>>/usr/lib/libfftw3l_threads.so.3
>>/usr/lib/libfftw3l_threads.so.3.2.4
>>/usr/share/doc/libfftw3-3
>>/usr/share/doc/libfftw3-3/NEWS.gz
>>/usr/share/doc/libfftw3-3/README
>>/usr/share/doc/libfftw3-3/README.Debian
>>/usr/share/doc/libfftw3-3/changelog.Debian.gz
>>/usr/share/doc/libfftw3-3/changelog.gz
>>/usr/share/doc/libfftw3-3/copyright
>>/var/cache/apt/archives/libfftw3-3_3.2.2-1_i386.deb
>>/var/lib/dpkg/info/libfftw3-3.list
>>/var/lib/dpkg/info/libfftw3-3.md5sums
>>/var/lib/dpkg/info/libfftw3-3.postinst
>>/var/lib/dpkg/info/libfftw3-3.postrm
>>/var/lib/dpkg/info/libfftw3-3.shlib
>>
>>
>>However, when I try installing Gromacs 4.5.3 the -/configure
>>step yields:
>>
>>configure: error: Cannot find fftw3f library
>>
>>
>>What am I doing incorrectly?
>>
>>
>>Without seeing the command you gave to configure, it's impossible to
>>say.
>>
>>-Justin
>>
>>Sergio
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at
>>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>><mailto:gmx-users-requ...@gromacs.org>.
>>
>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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[gmx-users] Ubuntu Installation

2011-01-11 Thread Sergio Manzetti

Dear users, I have installed FFTW3 successfully, and confirmed its location
using locate:


/home/m/Desktop/gromacs-4.5.3/src/mdlib/gmx_fft_fftw3.c
/usr/lib/libfftw3.so.3
/usr/lib/libfftw3.so.3.2.4
/usr/lib/libfftw3_threads.so.3
/usr/lib/libfftw3_threads.so.3.2.4
/usr/lib/libfftw3f.so.3
/usr/lib/libfftw3f.so.3.2.4
/usr/lib/libfftw3f_threads.so.3
/usr/lib/libfftw3f_threads.so.3.2.4
/usr/lib/libfftw3l.so.3
/usr/lib/libfftw3l.so.3.2.4
/usr/lib/libfftw3l_threads.so.3
/usr/lib/libfftw3l_threads.so.3.2.4
/usr/share/doc/libfftw3-3
/usr/share/doc/libfftw3-3/NEWS.gz
/usr/share/doc/libfftw3-3/README
/usr/share/doc/libfftw3-3/README.Debian
/usr/share/doc/libfftw3-3/changelog.Debian.gz
/usr/share/doc/libfftw3-3/changelog.gz
/usr/share/doc/libfftw3-3/copyright
/var/cache/apt/archives/libfftw3-3_3.2.2-1_i386.deb
/var/lib/dpkg/info/libfftw3-3.list
/var/lib/dpkg/info/libfftw3-3.md5sums
/var/lib/dpkg/info/libfftw3-3.postinst
/var/lib/dpkg/info/libfftw3-3.postrm
/var/lib/dpkg/info/libfftw3-3.shlib


However, when I try installing Gromacs 4.5.3 the -/configure step yields:

configure: error: Cannot find fftw3f library


What am I doing incorrectly?

Sergio
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Re: [gmx-users] Installation GROMACS UBUNTU

2010-12-24 Thread Sergio Manzetti

Thanks, but I will start from scratch.

On Fri, Dec 24, 2010 at 3:13 PM, Justin A. Lemkul  wrote:

> Quoting Sergio Manzetti :
>
> > Justin, THe FFTW messagte was AFTER sudo make install.
> >
>
> Then you're not an admin. You can always do the installations in your home
> directory (for both FFTW and Gromacs) by specifying an appropriate --prefix
> during configuration.
>
> -Justin
>
> > On Fri, Dec 24, 2010 at 2:53 PM, Sergio Manzetti <
> > sergio.manze...@vestforsk.no> wrote:
> >
> > > Well here is the FFTW message at make install:
> > >
> > >  /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h'
> > > /usr/bin/install: cannot remove `/usr/local/include/fftw3.h':
> Permission
> > > denied
> > >  /usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f'
> > > /usr/bin/install: cannot remove `/usr/local/include/fftw3.f':
> Permission
> > > denied
> > > make[3]: *** [install-includeHEADERS] Error 1
> > > make[3]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api'
> > > make[2]: *** [install-am] Error 2
> > > make[2]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api'
> > > make[1]: *** [install] Error 2
> > > make[1]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api'
> > >
> > >
> > >
> >
>
>
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] Installation GROMACS UBUNTU

2010-12-24 Thread Sergio Manzetti

Justin, THe FFTW messagte was AFTER sudo make install.

On Fri, Dec 24, 2010 at 2:53 PM, Sergio Manzetti <
sergio.manze...@vestforsk.no> wrote:

> Well here is the FFTW message at make install:
>
>  /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h'
> /usr/bin/install: cannot remove `/usr/local/include/fftw3.h': Permission
> denied
>  /usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f'
> /usr/bin/install: cannot remove `/usr/local/include/fftw3.f': Permission
> denied
> make[3]: *** [install-includeHEADERS] Error 1
> make[3]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api'
> make[2]: *** [install-am] Error 2
> make[2]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api'
> make[1]: *** [install] Error 2
> make[1]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api'
>
>
>
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Re: [gmx-users] Installation GROMACS UBUNTU

2010-12-24 Thread Sergio Manzetti

Well here is the FFTW message at make install:

 /usr/bin/install -c -m 644 'fftw3.h' '/usr/local/include/fftw3.h'
/usr/bin/install: cannot remove `/usr/local/include/fftw3.h': Permission
denied
 /usr/bin/install -c -m 644 'fftw3.f' '/usr/local/include/fftw3.f'
/usr/bin/install: cannot remove `/usr/local/include/fftw3.f': Permission
denied
make[3]: *** [install-includeHEADERS] Error 1
make[3]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/home/sergio/Desktop/fftw-3.2.2/api'
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Re: [gmx-users] Installation GROMACS UBUNTU

2010-12-24 Thread Sergio Manzetti

Thanks again J, is that compulsory each time one installs something new?

On Fri, Dec 24, 2010 at 2:50 PM, Justin A. Lemkul  wrote:

> Quoting Sergio Manzetti :
>
> > Thanks J, I think I will install Ubuntu entirely first, because I just
> tried
> > to install FFTW now, and managed only to get to make install, then I got
> > permission denied messages, so even though I thought I was the admin, I
> am
> > seemingly not.
> >
>
> Before blowing away your system, use "sudo make install," which will prompt
> you
> for your password and should work if you actually are an admin.
>
> -Justin
>
> > On Fri, Dec 24, 2010 at 2:44 PM, Justin A. Lemkul 
> wrote:
> >
> > > Quoting Sergio Manzetti :
> > >
> > > > Thanks Justin, here is it the copy-out:
> > > >
> > > > ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure
> > > > checking build system type... i686-pc-linux-gnu
> > > > checking host system type... i686-pc-linux-gnu
> > > > checking for a BSD-compatible install... /usr/bin/install -c
> > > > checking whether build environment is sane... yes
> > > > checking for a thread-safe mkdir -p... /bin/mkdir -p
> > > > checking for gawk... gawk
> > > > checking whether make sets $(MAKE)... yes
> > > > checking how to create a ustar tar archive... gnutar
> > > > checking for cc... cc
> > > > checking for C compiler default output file name... a.out
> > > > checking whether the C compiler works... yes
> > > > checking whether we are cross compiling... no
> > > > checking for suffix of executables...
> > > > checking for suffix of object files... o
> > > > checking whether we are using the GNU C compiler... yes
> > > > checking whether cc accepts -g... yes
> > > > checking for cc option to accept ISO C89... none needed
> > > > checking for style of include used by make... GNU
> > > > checking dependency style of cc... gcc3
> > > > checking dependency style of cc... gcc3
> > > > checking how to run the C preprocessor... cc -E
> > > > checking for grep that handles long lines and -e... /bin/grep
> > > > checking for egrep... /bin/grep -E
> > > > checking whether ln -s works... yes
> > > > checking whether cc accepts -O3... yes
> > > > checking whether cc accepts -msse2... yes
> > > > checking whether cc accepts -funroll-all-loops... yes
> > > > checking whether cc accepts -std=gnu99... yes
> > > > checking whether cc accepts -fexcess-precision=fast... no
> > > > checking whether cc accepts  -O3 -fomit-frame-pointer
> -finline-functions
> > > > -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes
> > > > checking for ANSI C header files... yes
> > > > checking for sys/types.h... yes
> > > > checking for sys/stat.h... yes
> > > > checking for stdlib.h... yes
> > > > checking for string.h... yes
> > > > checking for memory.h... yes
> > > > checking for strings.h... yes
> > > > checking for inttypes.h... yes
> > > > checking for stdint.h... yes
> > > > checking for unistd.h... yes
> > > > checking for unistd.h... (cached) yes
> > > > checking sys/time.h usability... yes
> > > > checking sys/time.h presence... yes
> > > > checking for sys/time.h... yes
> > > > checking sched.h usability... yes
> > > > checking sched.h presence... yes
> > > > checking for sched.h... yes
> > > > checking for sysconf... yes
> > > > checking for the pthreads library -lpthreads... no
> > > > checking whether pthreads work without any flags... no
> > > > checking whether pthreads work with -Kthread... no
> > > > checking whether pthreads work with -kthread... no
> > > > checking for the pthreads library -llthread... no
> > > > checking whether pthreads work with -pthread... yes
> > > > checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
> > > > checking if more special flags are required for pthreads... no
> > > > checking for cc_r... cc
> > > > checking if atomic operations are supported... yes
> > > > checking whether byte ordering is bigendian... no
> > > > checking that size_t can hold pointers... yes
> > > > checking for SIGUSR1... yes
> > > > checking for pipes... yes
> > > > checking floating-point format... IEEE754 (lit

Re: [gmx-users] Installation GROMACS UBUNTU

2010-12-24 Thread Sergio Manzetti

Thanks J, I think I will install Ubuntu entirely first, because I just tried
to install FFTW now, and managed only to get to make install, then I got
permission denied messages, so even though I thought I was the admin, I am
seemingly not.

On Fri, Dec 24, 2010 at 2:44 PM, Justin A. Lemkul  wrote:

> Quoting Sergio Manzetti :
>
> > Thanks Justin, here is it the copy-out:
> >
> > ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure
> > checking build system type... i686-pc-linux-gnu
> > checking host system type... i686-pc-linux-gnu
> > checking for a BSD-compatible install... /usr/bin/install -c
> > checking whether build environment is sane... yes
> > checking for a thread-safe mkdir -p... /bin/mkdir -p
> > checking for gawk... gawk
> > checking whether make sets $(MAKE)... yes
> > checking how to create a ustar tar archive... gnutar
> > checking for cc... cc
> > checking for C compiler default output file name... a.out
> > checking whether the C compiler works... yes
> > checking whether we are cross compiling... no
> > checking for suffix of executables...
> > checking for suffix of object files... o
> > checking whether we are using the GNU C compiler... yes
> > checking whether cc accepts -g... yes
> > checking for cc option to accept ISO C89... none needed
> > checking for style of include used by make... GNU
> > checking dependency style of cc... gcc3
> > checking dependency style of cc... gcc3
> > checking how to run the C preprocessor... cc -E
> > checking for grep that handles long lines and -e... /bin/grep
> > checking for egrep... /bin/grep -E
> > checking whether ln -s works... yes
> > checking whether cc accepts -O3... yes
> > checking whether cc accepts -msse2... yes
> > checking whether cc accepts -funroll-all-loops... yes
> > checking whether cc accepts -std=gnu99... yes
> > checking whether cc accepts -fexcess-precision=fast... no
> > checking whether cc accepts  -O3 -fomit-frame-pointer -finline-functions
> > -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes
> > checking for ANSI C header files... yes
> > checking for sys/types.h... yes
> > checking for sys/stat.h... yes
> > checking for stdlib.h... yes
> > checking for string.h... yes
> > checking for memory.h... yes
> > checking for strings.h... yes
> > checking for inttypes.h... yes
> > checking for stdint.h... yes
> > checking for unistd.h... yes
> > checking for unistd.h... (cached) yes
> > checking sys/time.h usability... yes
> > checking sys/time.h presence... yes
> > checking for sys/time.h... yes
> > checking sched.h usability... yes
> > checking sched.h presence... yes
> > checking for sched.h... yes
> > checking for sysconf... yes
> > checking for the pthreads library -lpthreads... no
> > checking whether pthreads work without any flags... no
> > checking whether pthreads work with -Kthread... no
> > checking whether pthreads work with -kthread... no
> > checking for the pthreads library -llthread... no
> > checking whether pthreads work with -pthread... yes
> > checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
> > checking if more special flags are required for pthreads... no
> > checking for cc_r... cc
> > checking if atomic operations are supported... yes
> > checking whether byte ordering is bigendian... no
> > checking that size_t can hold pointers... yes
> > checking for SIGUSR1... yes
> > checking for pipes... yes
> > checking floating-point format... IEEE754 (little-endian byte and word
> > order)
> > checking whether ln -s works... yes
> > checking whether make sets $(MAKE)... (cached) yes
> > checking for a sed that does not truncate output... /bin/sed
> > checking for ld used by cc ... /usr/bin/ld
> > checking if the linker (/usr/bin/ld) is GNU ld... yes
> > checking for /usr/bin/ld option to reload object files... -r
> > checking for BSD-compatible nm... /usr/bin/nm -B
> > checking how to recognise dependent libraries... pass_all
> > checking dlfcn.h usability... yes
> > checking dlfcn.h presence... yes
> > checking for dlfcn.h... yes
> > checking for g++... no
> > checking for c++... no
> > checking for gpp... no
> > checking for aCC... no
> > checking for CC... no
> > checking for cxx... no
> > checking for cc++... no
> > checking for cl.exe... no
> > checking for FCC... no
> > checking for KCC... no
> > checking for RCC... no
> > checking for xlC_r... no
> > checking for xlC... no
> > checking whether we are using the GNU

Re: [gmx-users] Installation GROMACS UBUNTU

2010-12-24 Thread Sergio Manzetti

Thanks Justin, here is it the copy-out:

ser...@sergio-laptop:~/Desktop/gromacs-4.5.3$ ./configure
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking for cc... cc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of cc... gcc3
checking dependency style of cc... gcc3
checking how to run the C preprocessor... cc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether ln -s works... yes
checking whether cc accepts -O3... yes
checking whether cc accepts -msse2... yes
checking whether cc accepts -funroll-all-loops... yes
checking whether cc accepts -std=gnu99... yes
checking whether cc accepts -fexcess-precision=fast... no
checking whether cc accepts  -O3 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for unistd.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sched.h usability... yes
checking sched.h presence... yes
checking for sched.h... yes
checking for sysconf... yes
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... cc
checking if atomic operations are supported... yes
checking whether byte ordering is bigendian... no
checking that size_t can hold pointers... yes
checking for SIGUSR1... yes
checking for pipes... yes
checking floating-point format... IEEE754 (little-endian byte and word
order)
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /bin/sed
checking for ld used by cc ... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl.exe... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
checking dependency style of g++... none
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from cc  object... failed
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if cc  supports -fno-rtti -fno-exceptions... no
checking for cc  option to produce PIC... -fPIC
checking if cc  PIC flag -fPIC works... yes
checking if cc  static flag -static works... yes
checking if cc  supports -c -o file.o... yes
checking whether the cc  linker (/usr/bin/ld) supports shared libraries...
yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
configure: creating li

Re: [gmx-users] Installation GROMACS UBUNTU

2010-12-24 Thread Sergio Manzetti

Not really, there were no errors with ./configure

so I downloaded the version through ubunto sudo -apt get install gromacs

but it was old version



On Fri, Dec 24, 2010 at 10:53 AM, Mark Abraham wrote:

>  On 24/12/2010 6:45 PM, Sergio Manzetti wrote:
>
> Hi thanks, but if I use make it says make no Makefile found...
>
>
> Right, so configure didn't work, unlike your statement that it did work...
> Troubleshoot the step that failed, not things that came after it...
>
> Mark
>
>
>
> On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham wrote:
>
>> On 23/12/2010 9:12 PM, Sergio Manzetti wrote:
>>
>>>
>>>
>>>
>>>
>>> Dear Users, I am unable to get pass the first step of ./configure . This
>>> step works, but when typing "make" it says:
>>>
>>> no targets specified and no makefile found.
>>>
>>
>>  That suggests configure did not work.
>>
>>
>>  Should it be like this, or is it compulsory to use cmake?
>>>
>>
>>  cmake is not compulsory.
>>
>> Mark
>>  --
>>   gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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[gmx-users] Updating Ubuntu

2010-12-24 Thread Sergio Manzetti

Dear all, I downloaded GMX from Ubuntu, and it was the 4.0.71 version. Does
anyone know or have the possibility to update UBUNTU with the latest GMX?

Cheers

Sergio
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Re: [gmx-users] Installation GROMACS UBUNTU

2010-12-23 Thread Sergio Manzetti

Hi thanks, but if I use make it says make no Makefile found...



On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham wrote:

> On 23/12/2010 9:12 PM, Sergio Manzetti wrote:
>
>>
>>
>>
>>
>> Dear Users, I am unable to get pass the first step of ./configure . This
>> step works, but when typing "make" it says:
>>
>> no targets specified and no makefile found.
>>
>
> That suggests configure did not work.
>
>
>  Should it be like this, or is it compulsory to use cmake?
>>
>
> cmake is not compulsory.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
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[gmx-users] Grompp error message

2010-12-23 Thread Sergio Manzetti

Dear users,

I made the a topology, but when I grompp for EM I get this weird message:

Fatal error:
Syntax error - File forcefield.itp, line 12
Last line read:
'Buckingham  1  no   1.0 1.0'
Found a second defaults directive.


I attached the topology here with the gro file. Does anybody recognize this
message?

Best wishes

Sergio


bzp.itp
Description: Binary data


bzp.gro
Description: Binary data
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[gmx-users] Installation GROMACS UBUNTU

2010-12-23 Thread Sergio Manzetti

Dear Users, I am unable to get pass the first step of ./configure . This
step works, but when typing "make" it says:

no targets specified and no makefile found.

Should it be like this, or is it compulsory to use cmake?
-- 
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Re: [gmx-users] Silly question?

2010-12-22 Thread Sergio Manzetti

   222425 1  1.20e+02  4.00e+02  1.20e+02
4.00e+02
   222426 1  1.20e+02  4.00e+02  1.20e+02
4.00e+02
   252426 1  1.20e+02  4.00e+02  1.20e+02
4.00e+02
   242627 1  1.20e+02  4.00e+02  1.20e+02
4.00e+02
   242628 1  1.20e+02  4.00e+02  1.20e+02
4.00e+02
   272628 1  1.20e+02  4.00e+02  1.20e+02
4.00e+02
12826 1  1.20e+02  4.00e+02  1.20e+02
4.00e+02
12829 1  1.21e+02  4.00e+02  1.21e+02
4.00e+02
   262829 1  1.20e+02  4.00e+02  1.20e+02
4.00e+02
   282930 1  1.20e+02  4.00e+02  1.20e+02
4.00e+02
   282931 1  1.20e+02  4.00e+02  1.20e+02
4.00e+02
   302931 1  1.20e+02  4.00e+02  1.20e+02
4.00e+02
33129 1  1.22e+02  4.00e+02  1.22e+02
4.00e+02
33132 1  1.19e+02  4.00e+02  1.19e+02
4.00e+02
   293132 1  1.19e+02  4.00e+02  1.19e+02
4.00e+02

[ dihedrals ]
;  aiajakal functc0c1
c2c3
1 22128 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
2 1 316 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
3 2 431 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
4 3 513 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
5 4 6 7 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
7 5 8 9 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
9 71011 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
   11 91213 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
   13 41114 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
   14131516 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
   16 21417 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
   17161819 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
   19172021 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
   21 11922 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
   22212324 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
   24222526 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
   26242728 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
   28 12629 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
   29283031 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00
   31 32932 1  1.80e+02  5.00e+00  1.80e+02
5.00e+00



On Wed, Dec 22, 2010 at 7:36 PM, Justin A. Lemkul  wrote:

>
>
> Sergio Manzetti wrote:
>
>>
>>
>>
>> I am trying to grompp a molecule, but get the same error again:
>>
>> Program grompp, VERSION 4.5.1
>> Source code file: topio.c, line: 654
>>
>> Fatal error:
>> Syntax error - File bzp.itp, line 1
>> Last line read:
>> '[ moleculetype ]'
>> Invalid order for directive moleculetype
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> Can any help?
>>
>>
> Something in your topology is out of order.  See Chapter 5 of the manual
> for the proper order.  Either you've #included one moleculetype inside
> another, or you've done it before the force field has defined.  Either way,
> if you want further assistance, you'll have to post some relevant snapshots
> of your topology.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
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>
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[gmx-users] Silly question?

2010-12-22 Thread Sergio Manzetti

I am trying to grompp a molecule, but get the same error again:

Program grompp, VERSION 4.5.1
Source code file: topio.c, line: 654

Fatal error:
Syntax error - File bzp.itp, line 1
Last line read:
'[ moleculetype ]'
Invalid order for directive moleculetype
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Can any help?
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Re: [gmx-users] where can I download POPC membrane file?

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Re: [gmx-users] Ubuntu Installation

Re: [gmx-users] Ubuntu Installation

[gmx-users] Ubuntu Installation

Re: [gmx-users] Installation GROMACS UBUNTU

Re: [gmx-users] Installation GROMACS UBUNTU

Re: [gmx-users] Installation GROMACS UBUNTU

Re: [gmx-users] Installation GROMACS UBUNTU

Re: [gmx-users] Installation GROMACS UBUNTU

Re: [gmx-users] Installation GROMACS UBUNTU

Re: [gmx-users] Installation GROMACS UBUNTU

[gmx-users] Updating Ubuntu

Re: [gmx-users] Installation GROMACS UBUNTU

[gmx-users] Grompp error message

[gmx-users] Installation GROMACS UBUNTU

Re: [gmx-users] Silly question?

[gmx-users] Silly question?

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