<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
--></style>
</head>
<body class='hmmessage'>
Dear Carsten Kutzner<br><br>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 :<br><br>p10_522: p4_error: Timeout in establishing connection to remote process: 0<br>p8_468: p4_error: Timeout in establishing connection to remote process: 0<br>p9_495: p4_error: Timeout in establishing connection to remote process: 0<br>p0_32740: p4_error: net_recv read: probable EOF on socket: 1<br>Killed by signal 2.<br>Killed by signal 2.<br>p4_359: p4_error: net_recv read: probable EOF on socket: 1<br>p6_413: p4_error: net_recv read: probable EOF on socket: 1<br>Killed by signal 2.<br>Killed by signal 2.<br>Killed by signal 2.<br>Killed by signal 2.<br>Killed by signal 2.<br>Killed by signal 2.<br>Killed by signal 2.<br>Killed by signal 2.<br>Killed by signal 2.<br>Killed by signal 2.<br>Killed by signal 2.<br>Killed by signal 2.<br>Killed by signal 2.<br><br>I dont know how to solve this problem. Any help in this respect will be by highly appreciated by our research group.<br><br>Many regards<br><br><br><div>Abdul Wadood, <br>Research Scholar, <br>Dr.Panjwani Center for Molecular Medicine and <br>Drug Research, <br>International Center for Chemical and <br>Biological Science, <br>University of Karachi, Karachi-75720, Pakistan. <br>Email:wadoodbiochemist@hotmail.com <br></div><br><br><br><br>> From: gmx-users-request@gromacs.org<br>> Subject: gmx-users Digest, Vol 74, Issue 76<br>> To: gmx-users@gromacs.org<br>> Date: Mon, 14 Jun 2010 10:49:39 +0200<br>> <br>> Send gmx-users mailing list submissions to<br>> gmx-users@gromacs.org<br>> <br>> To subscribe or unsubscribe via the World Wide Web, visit<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> or, via email, send a message with subject or body 'help' to<br>> gmx-users-request@gromacs.org<br>> <br>> You can reach the person managing the list at<br>> gmx-users-owner@gromacs.org<br>> <br>> When replying, please edit your Subject line so it is more specific<br>> than "Re: Contents of gmx-users digest..."<br>> <br>> <br>> Today's Topics:<br>> <br>> 1. Parallel installation (abdul wadood)<br>> 2. Re: No Energy Conservation in NVE simulation of liquid<br>> mixtures (Tsjerk Wassenaar)<br>> 3. Re: Parallel installation (Carsten Kutzner)<br>> 4. Re: soft-core (Sai Kumar Ramadugu)<br>> <br>> <br>> ----------------------------------------------------------------------<br>> <br>> Message: 1<br>> Date: Mon, 14 Jun 2010 05:20:35 +0000<br>> From: abdul wadood <wadoodbiochemist@hotmail.com><br>> Subject: [gmx-users] Parallel installation<br>> To: <gmx-users@gromacs.org><br>> Message-ID: <BAY121-W11B72195B2499F884941E2D0DC0@phx.gbl><br>> Content-Type: text/plain; charset="iso-8859-1"<br>> <br>> <br>> Hello,<br>> <br>> I am new user of gromacs. I have installed the gromacs and enable the mpi but when I run the command<br>> <br>> "mpirun -np 12 mdrun_mpi -s topol.tpr -o test.trr -x test.xtc -c confout.gro -e test.edr -g test.log"<br>> <br>> The error come that <br>> <br>> "Program mdrun_mpi either does not exist, is not<br>> executable, or is an erroneous argument to mpirun."<br>> <br>> 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.<br>> <br>> Your help will be highly appreciated by our research group.<br>> <br>> Many regards<br>> <br>> Abdul Wadood, <br>> Research Scholar, <br>> Dr.Panjwani Center for Molecular Medicine and <br>> Drug Research, <br>> International Center for Chemical and <br>> Biological Science, <br>> University of Karachi, Karachi-75720, Pakistan. <br>> Email:wadoodbiochemist@hotmail.com <br>> <br>> <br>> <br>> _________________________________________________________________<br>> Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox.<br>> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1<br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100614/5099f86b/attachment-0001.html<br>> <br>> ------------------------------<br>> <br>> Message: 2<br>> Date: Mon, 14 Jun 2010 08:19:30 +0200<br>> From: Tsjerk Wassenaar <tsjerkw@gmail.com><br>> Subject: Re: [gmx-users] No Energy Conservation in NVE simulation of<br>> liquid mixtures<br>> To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> Message-ID:<br>> <AANLkTimamtQEICdB-aczZMr8LykO2UmcO20A4JoZa6Ij@mail.gmail.com><br>> Content-Type: text/plain; charset=ISO-8859-1<br>> <br>> Hi Godwin,<br>> <br>> I noticed you're removing center of mass motion, which you shouldn't for NVE.<br>> <br>> Cheers,<br>> <br>> Tsjerk<br>> <br>> On Mon, Jun 14, 2010 at 4:09 AM, Godwin Kanu <biggugo@live.com> wrote:<br>> ><br>> > Hi GMX Users,<br>> ><br>> > I am having difficulties getting gromacs to conserve energy (I experience a<br>> > directional drift) when I do an NVE simulation of mixtures (i tried both<br>> > THF/water and water/methanol). But when I do simulation of a pure liquid it<br>> > works great. I have tried tinkering with a lot of stuff including the<br>> > electrostatic interaction and making sure the combination rules for<br>> > non-bonded interactions work as it is supposed to. I usually start with an<br>> > NVT simulation to equilibriate it at the temperature I'm interested in<br>> > before removing the temperature bath to do an equilibration run in<br>> > the microcanonical ensemble. I have attached some of my input files for you<br>> > to examine. I'm using GROMACS version 4.0.5 parallel.<br>> > Thanks<br>> ><br>> > Godwin.<br>> ><br>> ><br>> ><br>> > ________________________________<br>> > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox.<br>> > Learn more.<br>> > --<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> <br>> <br>> <br>> -- <br>> Tsjerk A. Wassenaar, Ph.D.<br>> <br>> post-doctoral researcher<br>> Molecular Dynamics Group<br>> Groningen Institute for Biomolecular Research and Biotechnology<br>> University of Groningen<br>> The Netherlands<br>> <br>> <br>> ------------------------------<br>> <br>> Message: 3<br>> Date: Mon, 14 Jun 2010 10:00:50 +0200<br>> From: Carsten Kutzner <ckutzne@gwdg.de><br>> Subject: Re: [gmx-users] Parallel installation<br>> To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> Message-ID: <525E5819-5B8C-4403-9D55-7428BFAE1BFD@gwdg.de><br>> Content-Type: text/plain; charset="us-ascii"<br>> <br>> Hi,<br>> <br>> you either have to add the directory where mdrun_mpi resides to your<br>> path or you have to give mpirun the full path name of mdrun_mpi.<br>> <br>> You can add the Gromacs executables to your path by the command<br>> <br>> source /path/to/your/installed/gromacs/bin/GMXRC<br>> <br>> Or use<br>> <br>> mpirun -np 12 /path/to/your/installed/gromacs/bin/mdrun_mpi -s topol.tpr ...<br>> <br>> Carsten<br>> <br>> <br>> <br>> On Jun 14, 2010, at 7:20 AM, abdul wadood wrote:<br>> <br>> > Hello,<br>> > <br>> > I am new user of gromacs. I have installed the gromacs and enable the mpi but when I run the command<br>> > <br>> > "mpirun -np 12 mdrun_mpi -s topol.tpr -o test.trr -x test.xtc -c confout.gro -e test.edr -g test.log"<br>> > <br>> > The error come that <br>> > <br>> > "Program mdrun_mpi either does not exist, is not<br>> > executable, or is an erroneous argument to mpirun."<br>> > <br>> > 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.<br>> > <br>> > Your help will be highly appreciated by our research group.<br>> > <br>> > Many regards<br>> > <br>> > Abdul Wadood, <br>> > Research Scholar, <br>> > Dr.Panjwani Center for Molecular Medicine and <br>> > Drug Research, <br>> > International Center for Chemical and <br>> > Biological Science, <br>> > University of Karachi, Karachi-75720, Pakistan. <br>> > Email:wadoodbiochemist@hotmail.com <br>> > <br>> > <br>> > <br>> > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. Learn more. -- <br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> <br>> --<br>> Dr. Carsten Kutzner<br>> Max Planck Institute for Biophysical Chemistry<br>> Theoretical and Computational Biophysics<br>> Am Fassberg 11, 37077 Goettingen, Germany<br>> Tel. +49-551-2012313, Fax: +49-551-2012302<br>> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne<br>> <br>> <br>> <br>> <br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100614/7b6329cd/attachment-0001.html<br>> <br>> ------------------------------<br>> <br>> Message: 4<br>> Date: Mon, 14 Jun 2010 03:48:46 -0500<br>> From: Sai Kumar Ramadugu <sramadugu@gmail.com><br>> Subject: Re: [gmx-users] soft-core<br>> To: jalemkul@vt.edu, Discussion list for GROMACS users<br>> <gmx-users@gromacs.org><br>> Message-ID:<br>> <AANLkTikQNVfOGypzNW-MZ6j-ZPHogWQKGv4POL9jsmLs@mail.gmail.com><br>> Content-Type: text/plain; charset="iso-8859-1"<br>> <br>> Hi<br>> Well the tutorial in the following website has mentioned about the<br>> importance of sc_alpha and sc-power. Also the manual gives you more<br>> information.<br>> http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial.<br>> <br>> Regards<br>> Sai<br>> <br>> On Sun, Jun 13, 2010 at 6:56 PM, Justin A. Lemkul <jalemkul@vt.edu> wrote:<br>> <br>> ><br>> ><br>> > fancy2012 wrote:<br>> ><br>> >> Dear GMX users,<br>> >> when I generate the input file of MD simulation using grompp, I get this<br>> >> error: ERROR: The soft-core power is 0 and can only be 1 or 2. I don't know<br>> >> how to figure it out? Could somebody give me a hand? Thanks very much in<br>> >> advance!<br>> >><br>> ><br>> > You haven't specified a value for sc-power, so the default of zero is<br>> > taken. Manual section 7.3.23.<br>> ><br>> > -Justin<br>> ><br>> > Here is the mdp file:<br>> >> cpp = /lib/cpp<br>> >> constraints = all-bonds<br>> >> integrator = md<br>> >> tinit = 0.0<br>> >> dt = 0.002 nsteps = 25000 nstcomm<br>> >> = 1<br>> >> nstxout = 10000<br>> >> nstvout = 0<br>> >> nstfout = 0<br>> >> nstlog = 500<br>> >> nstenergy = 250<br>> >> nstxtcout = 1000<br>> >> xtc_precision = 1000<br>> >> xtc_grps = Protein<br>> >> nstlist = 5<br>> >> energygrps = Protein SOL<br>> >> ns_type = grid<br>> >> rlist = 0.9<br>> >> coulombtype = Reaction-Field<br>> >> epsilon_r = 78.0<br>> >> rcoulomb = 1.4<br>> >> rvdw = 1.4<br>> >> Tcoupl = Berendsen<br>> >> tc-grps = Protein SOL<br>> >> ref_t = 300 300<br>> >> tau_t = 0.1 0.1<br>> >> Pcoupl = Berendsen<br>> >> tau_p = 1.0<br>> >> compressibility = 4.6e-5<br>> >> ref_p ; = 1.0<br>> >><br>> >> free_energy = yes<br>> >> init_lambda = 0.00<br>> >> sc-alpha = 1.51<br>> >> All the best,<br>> >> fancy<br>> >><br>> >><br>> ><br>> > --<br>> > ========================================<br>> ><br>> > Justin A. Lemkul<br>> > Ph.D. Candidate<br>> > ICTAS Doctoral Scholar<br>> > MILES-IGERT Trainee<br>> > Department of Biochemistry<br>> > Virginia Tech<br>> > Blacksburg, VA<br>> > jalemkul[at]vt.edu | (540) 231-9080<br>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> ><br>> > ========================================<br>> > --<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the www interface<br>> > or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100614/50ea765c/attachment.html<br>> <br>> ------------------------------<br>> <br>> -- <br>> gmx-users mailing list<br>> gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> <br>> End of gmx-users Digest, Vol 74, Issue 76<br>> *****************************************<br> <br /><hr />Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. <a href='http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1' target='_new'>Learn more.</a></body>
</html>