[gmx-users] Parallel instalation: gmx-users Digest, Vol 74, Issue 76
abdul wadood
wadoodbiochemist at hotmail.com
Tue Jun 15 10:10:07 CEST 2010
Dear Carsten Kutzner
First, I am very thankful to you and highly appreciate your help. According to your guideness I given the path for mdrun_mpi and the command run successfully. But now the problem is the simulation run for some time and the killed and give the error which is :
p10_522: p4_error: Timeout in establishing connection to remote process: 0
p8_468: p4_error: Timeout in establishing connection to remote process: 0
p9_495: p4_error: Timeout in establishing connection to remote process: 0
p0_32740: p4_error: net_recv read: probable EOF on socket: 1
Killed by signal 2.
Killed by signal 2.
p4_359: p4_error: net_recv read: probable EOF on socket: 1
p6_413: p4_error: net_recv read: probable EOF on socket: 1
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
I dont know how to solve this problem. Any help in this respect will be by highly appreciated by our research group.
Many regards
Abdul Wadood,
Research Scholar,
Dr.Panjwani Center for Molecular Medicine and
Drug Research,
International Center for Chemical and
Biological Science,
University of Karachi, Karachi-75720, Pakistan.
Email:wadoodbiochemist at hotmail.com
> From: gmx-users-request at gromacs.org
> Subject: gmx-users Digest, Vol 74, Issue 76
> To: gmx-users at gromacs.org
> Date: Mon, 14 Jun 2010 10:49:39 +0200
>
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Parallel installation (abdul wadood)
> 2. Re: No Energy Conservation in NVE simulation of liquid
> mixtures (Tsjerk Wassenaar)
> 3. Re: Parallel installation (Carsten Kutzner)
> 4. Re: soft-core (Sai Kumar Ramadugu)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 14 Jun 2010 05:20:35 +0000
> From: abdul wadood <wadoodbiochemist at hotmail.com>
> Subject: [gmx-users] Parallel installation
> To: <gmx-users at gromacs.org>
> Message-ID: <BAY121-W11B72195B2499F884941E2D0DC0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hello,
>
> I am new user of gromacs. I have installed the gromacs and enable the mpi but when I run the command
>
> "mpirun -np 12 mdrun_mpi -s topol.tpr -o test.trr -x test.xtc -c confout.gro -e test.edr -g test.log"
>
> The error come that
>
> "Program mdrun_mpi either does not exist, is not
> executable, or is an erroneous argument to mpirun."
>
> I have search the problem on mailing list but I do not found satisfactory answer to solve my problem. If you kindly help me in this respect I will be very thankful to you.
>
> Your help will be highly appreciated by our research group.
>
> Many regards
>
> Abdul Wadood,
> Research Scholar,
> Dr.Panjwani Center for Molecular Medicine and
> Drug Research,
> International Center for Chemical and
> Biological Science,
> University of Karachi, Karachi-75720, Pakistan.
> Email:wadoodbiochemist at hotmail.com
>
>
>
> _________________________________________________________________
> Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox.
> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100614/5099f86b/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Mon, 14 Jun 2010 08:19:30 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] No Energy Conservation in NVE simulation of
> liquid mixtures
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTimamtQEICdB-aczZMr8LykO2UmcO20A4JoZa6Ij at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Godwin,
>
> I noticed you're removing center of mass motion, which you shouldn't for NVE.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Jun 14, 2010 at 4:09 AM, Godwin Kanu <biggugo at live.com> wrote:
> >
> > Hi GMX Users,
> >
> > I am having difficulties getting gromacs to conserve energy (I experience a
> > directional drift) when I do an NVE simulation of mixtures (i tried both
> > THF/water and water/methanol). But when I do simulation of a pure liquid it
> > works great. I have tried tinkering with a lot of stuff including the
> > electrostatic interaction and making sure the combination rules for
> > non-bonded interactions work as it is supposed to. I usually start with an
> > NVT simulation to equilibriate it at the temperature I'm interested in
> > before removing the temperature bath to do an equilibration run in
> > the microcanonical ensemble. I have attached some of my input files for you
> > to examine. I'm using GROMACS version 4.0.5 parallel.
> > Thanks
> >
> > Godwin.
> >
> >
> >
> > ________________________________
> > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox.
> > Learn more.
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology
> University of Groningen
> The Netherlands
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 14 Jun 2010 10:00:50 +0200
> From: Carsten Kutzner <ckutzne at gwdg.de>
> Subject: Re: [gmx-users] Parallel installation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <525E5819-5B8C-4403-9D55-7428BFAE1BFD at gwdg.de>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> you either have to add the directory where mdrun_mpi resides to your
> path or you have to give mpirun the full path name of mdrun_mpi.
>
> You can add the Gromacs executables to your path by the command
>
> source /path/to/your/installed/gromacs/bin/GMXRC
>
> Or use
>
> mpirun -np 12 /path/to/your/installed/gromacs/bin/mdrun_mpi -s topol.tpr ...
>
> Carsten
>
>
>
> On Jun 14, 2010, at 7:20 AM, abdul wadood wrote:
>
> > Hello,
> >
> > I am new user of gromacs. I have installed the gromacs and enable the mpi but when I run the command
> >
> > "mpirun -np 12 mdrun_mpi -s topol.tpr -o test.trr -x test.xtc -c confout.gro -e test.edr -g test.log"
> >
> > The error come that
> >
> > "Program mdrun_mpi either does not exist, is not
> > executable, or is an erroneous argument to mpirun."
> >
> > I have search the problem on mailing list but I do not found satisfactory answer to solve my problem. If you kindly help me in this respect I will be very thankful to you.
> >
> > Your help will be highly appreciated by our research group.
> >
> > Many regards
> >
> > Abdul Wadood,
> > Research Scholar,
> > Dr.Panjwani Center for Molecular Medicine and
> > Drug Research,
> > International Center for Chemical and
> > Biological Science,
> > University of Karachi, Karachi-75720, Pakistan.
> > Email:wadoodbiochemist at hotmail.com
> >
> >
> >
> > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. Learn more. --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
>
>
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100614/7b6329cd/attachment-0001.html
>
> ------------------------------
>
> Message: 4
> Date: Mon, 14 Jun 2010 03:48:46 -0500
> From: Sai Kumar Ramadugu <sramadugu at gmail.com>
> Subject: Re: [gmx-users] soft-core
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTikQNVfOGypzNW-MZ6j-ZPHogWQKGv4POL9jsmLs at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi
> Well the tutorial in the following website has mentioned about the
> importance of sc_alpha and sc-power. Also the manual gives you more
> information.
> http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial.
>
> Regards
> Sai
>
> On Sun, Jun 13, 2010 at 6:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > fancy2012 wrote:
> >
> >> Dear GMX users,
> >> when I generate the input file of MD simulation using grompp, I get this
> >> error: ERROR: The soft-core power is 0 and can only be 1 or 2. I don't know
> >> how to figure it out? Could somebody give me a hand? Thanks very much in
> >> advance!
> >>
> >
> > You haven't specified a value for sc-power, so the default of zero is
> > taken. Manual section 7.3.23.
> >
> > -Justin
> >
> > Here is the mdp file:
> >> cpp = /lib/cpp
> >> constraints = all-bonds
> >> integrator = md
> >> tinit = 0.0
> >> dt = 0.002 nsteps = 25000 nstcomm
> >> = 1
> >> nstxout = 10000
> >> nstvout = 0
> >> nstfout = 0
> >> nstlog = 500
> >> nstenergy = 250
> >> nstxtcout = 1000
> >> xtc_precision = 1000
> >> xtc_grps = Protein
> >> nstlist = 5
> >> energygrps = Protein SOL
> >> ns_type = grid
> >> rlist = 0.9
> >> coulombtype = Reaction-Field
> >> epsilon_r = 78.0
> >> rcoulomb = 1.4
> >> rvdw = 1.4
> >> Tcoupl = Berendsen
> >> tc-grps = Protein SOL
> >> ref_t = 300 300
> >> tau_t = 0.1 0.1
> >> Pcoupl = Berendsen
> >> tau_p = 1.0
> >> compressibility = 4.6e-5
> >> ref_p ; = 1.0
> >>
> >> free_energy = yes
> >> init_lambda = 0.00
> >> sc-alpha = 1.51
> >> All the best,
> >> fancy
> >>
> >>
> >
> > --
> > ========================================
> >
> > 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 list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the www interface
> > or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100614/50ea765c/attachment.html
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 74, Issue 76
> *****************************************
_________________________________________________________________
Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox.
http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100615/90837406/attachment.html>
More information about the gromacs.org_gmx-users
mailing list