[gmx-users] Re: Segmentation falt error - installing gromacs-3.3.1 on Mac-OSX
Ibrahim M. Moustafa
I.moustafa at psu.edu
Mon Dec 4 17:05:43 CET 2006
Hi David,
Yes, I did source $GMXBIN/GMXRC or GMXRC.csh (for my tcsh) to
setup the environment. This did not solve the problem.
thanks,
Ibrahim
At 04:26 AM 12/2/2006, you wrote:
>Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
> http://www.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. Surface Tension of a lipid bilayer (toma0052)
> 2. opls parameters (Komath Damodaran)
> 3. Segmentaion fault error- installing gromacs-3.3.1 on MacOSX
> (Ibrahim M. Moustafa)
> 4. Question about NVT (Justin Lemkul)
> 5. References for globular protein simulation using PME (Dilraj Lama)
> 6. Re: Surface Tension of a lipid bilayer (David van der Spoel)
> 7. Re: Segmentaion fault error- installing gromacs-3.3.1 on
> MacOSX (David van der Spoel)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Fri, 01 Dec 2006 16:59:20 CST
>From: toma0052 <toma0052 at umn.edu>
>Subject: [gmx-users] Surface Tension of a lipid bilayer
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <200612012259.kB1MxKqM009043 at saturn.software.umn.edu>
>Content-Type: TEXT/plain; CHARSET=US-ASCII
>
>Hello,
> I have a question about calculating the surface tension for the
>water-lipid interface of a lipid bilayer. After an MD run, I can use my .edr
>file and g_energy to calculate the surface tension. I believe that the
>surface tension is calculated something like gamma = (Pzz-(Pxx+Pyy)/2)/L. I
>was wondering though, is the pressure tensor and hence surface tension
>calculated over the entire simulation box? I would assume so, since I did
>not specify any molecules. To find the water-lipid surface tension, would I
>not need to sum over only the molecules at the surface? Would this be
>do-able in Gromacs? Would I have to write something separate to do this?
> In my coordinate file, I have DPPC atoms, solvent atoms, and other atoms
>(those that make up the head group ie O,N etc.). Could I just make an index
>group that is not DPPC and not Solvent, and sum over those atoms?
>
>Thanks,
>Mike Tomasini
>
>
>
>------------------------------
>
>Message: 2
>Date: Fri, 1 Dec 2006 16:35:32 -0800
>From: "Komath Damodaran" <kdamodaran at telik.com>
>Subject: [gmx-users] opls parameters
>To: <gmx-users at gromacs.org>
>Message-ID:
>
><49C6E25ABA2A1347AF34522CF026A7F901D65479 at EXCHANGE02.TelikHQ.telik.com>
>
>Content-Type: text/plain; charset="us-ascii"
>
>Hi All,
>
>I am trying to build the itp file for a molecule. I would like to use
>the opls force field. The ffoplsaa.atp contains the atom types as
>opls_xxx. But the ffoplsbon.itp which contains the bond-angle-dihedral
>parameters does not use the opls_xxx convention. Is there a way to
>identify the bond/angle/torsion parameters of a set of opls_xxx atoms?
>
>
>
>Thanks very much!
>
>Dam
>
>-------------------------------------------
>
>Komath Damodaran
>
>Scientist, Computational Chemistry
>
>Telik, Inc.
>
>3165 Porter Drive
>
>Palo Alto, CA 94304
>
>Tel: (650) 845-7838, Fax: 650-845-7800
>
>===========================================
>
>This email message is for the sole use of the intended recipient(s) and
>may contain confidential and privileged information. Any unauthorized
>review, use, disclosure or distribution is prohibited. If you are not
>the intended recipient, please contact the sender by reply email and
>destroy all copies of the original message.
>
>============================================
>
>
>
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL:
>http://www.gromacs.org/pipermail/gmx-users/attachments/20061201/551ecc34/attachment-0001.html
>
>------------------------------
>
>Message: 3
>Date: Fri, 01 Dec 2006 21:15:18 -0500
>From: "Ibrahim M. Moustafa" <I.moustafa at psu.edu>
>Subject: [gmx-users] Segmentaion fault error- installing gromacs-3.3.1
> on MacOSX
>To: gmx-users at gromacs.org
>Message-ID: <7.0.1.0.0.20061201211510.02108110 at psu.edu>
>Content-Type: text/plain; charset="us-ascii"; format=flowed
>
>Hi gmx-users,
>
> I have a little problem with gromacs-3.3.1 installed on a Mac-OSX.
>After installation (either building the package myself as instructed,
>or using a binary form GROMACS web site) I could not run any program
>with just typing the name on the xterm!
>for example, issuing "pdb2gmx" command line gives an error message
>"segmentation fault". However, typing the whole path name
>"$GMXBIN/pdb2gmx or any other modules " works fine.
>The variables for GROMACS are configured after the installation. My
>.cshrc sources from the GMXRC.csh and the variables are defined; the
>PATH includes the $GMXBIN also.
>For the moment, I'm using alias to define the whole path for GROMACS
>programs to run; though, this a bit annoying.
>
> I posted this problem in CCL and M.L. Dodson, replied with some
>explanation for this weird problem:
>
> " Ahh... Think I have it. Looking at the source code on my BSD Unix
>box, I see in src/gmxlib/copyrite.c the following:
>
>void CopyRight(FILE *out,char *szProgram)
>{
> /* Dont change szProgram arbitrarily - it must be argv[0], i.e. the
> * name of a file. Otherwise, we won't be able to find the library dir.
> */
>#define NCR (int)asize(CopyrightText)
>#define NGPL (int)asize(GPLText)
>
> char buf[256],tmpstr[1024];
>
> char *ptr;
>
> int i;
>
> set_program_name(szProgram);
> .
> .
> .
>
>So I was right, it does use argv[0] for something: finding its
>library directory."
>
> I wonder if there is a quick fix for this in the code, so I can
>run the programs by just typing the name without need for the whole path!
>
> A question here: if Dodson is right, why the programer wrote the
>code this way! is there any advantage?
>
>P.S. I have no previous experience with GROMACS
>
> thanks,
> Ibrahim
>
>
>
>------------------------------
>
>Message: 4
>Date: Sat, 2 Dec 2006 00:07:48 -0500
>From: Justin Lemkul <jalemkul at vt.edu>
>Subject: [gmx-users] Question about NVT
>To: gmx-users at gromacs.org
>Message-ID: <1165036068.45710a24bd82f at webmail.vt.edu>
>Content-Type: text/plain; charset=ISO-8859-1
>
>Hello all,
>
>I have a quick question regarding an MD simulation I am attempting to run
>(again, the membrane protein which I had problems with previously). Thanks to
>the helpful suggestions; my system is now well-minimized! The last
>step before
>I would like to take before running full-out MD on my system is to equilibrate
>my solvent and ions over a short timeframe (100ps). My initial attempts have
>been unsuccessful; the equilibration proceeds nicely for 960 steps (1.920 ps)
>before I get a screen full of LINCS warnings. Apparently one of my DPPC
>molecules is being blown apart. I have placed position restraints on both my
>protein and my bilayer, in order to allow the solvent and ions (Na+) to move
>around them. I have attached my equil.mdp file below, in case I am making any
>obvious mistakes. I am piecing my .mdp file together from several
>examples and
>tutorials.
>
>My value for nstlog is set very small so I could monitor energies,
>etc after the
>first failure...in case anyone was wondering :)
>
>Thanks in advance for your kind advice in helping out a newbie.
>
>-Justin
>
>PS - I'm running Gromacs v3.3 on Mac OSX v10.4.8, in case any of that matters.
>
>----------
>title = MD equilibration of solvent and ions
>cpp = /usr/bin/cpp
>include = -I./
>define = -DPOSRES -DPOSRES_LIPID
>integrator = md
>nsteps = 50000
>nstlist = 10
>nstxout = 1000
>nstvout = 1000
>nstlog = 10
>nstenergy = 1000
>nstxtcout = 1000
>dt = 0.002
>ns_type = simple
>coulombtype = cut-off
>rlist = 0.9
>rvdw = 0.9
>rcoulomb = 0.9
>fourierspacing = 0.12
>; Temperature coupling is on in four groups
>tcoupl = berendsen
>tc_grps = Protein DPPC SOL NA+
>tau_t = 0.1 0.1 0.1 0.1
>ref_t = 323 323 323 323
>; Pressure coupling is not on
>Pcoupl = no
>ref_p = 1.0
>gen_vel = no
>gen_temp = 323
>constraints = all-bonds
>constraint_algorithm = lincs
>optimize_fft = yes
>DispCorr = EnerPres
>pbc = full
>---------
>
>Justin A. Lemkul
>Department of Biochemistry
>Virginia Tech
>
>
>------------------------------
>
>Message: 5
>Date: Sat, 2 Dec 2006 13:37:55 +0530 (IST)
>From: "Dilraj Lama" <dennis at iitk.ac.in>
>Subject: [gmx-users] References for globular protein simulation using
> PME
>To: gmx-users at gromacs.org
>Message-ID:
> <1373.172.26.89.79.1165046875.squirrel at newwebmail.iitk.ac.in>
>Content-Type: text/plain;charset=iso-8859-15
>
>
>Dear all gmx-users,
> I have been trying to dig out some well cited paper on
>simulation of globular protein using PME .Can anyone
>please suggest to me some references I can look out
>for.
>
>Thanks to all.
>
>--
>Dilraj Lama,
>Graduate student,
>Bioinformatics and Biomolecular Simualtion lab,
>Dept. of BSBE;IITK-kanpur,
>Uttar pradesh,India-208016.
>email:dennis at iitk.ac.in,dilraj2002 at yahoo.com
>mob:09415473973
>
>
>
>------------------------------
>
>Message: 6
>Date: Sat, 02 Dec 2006 10:22:21 +0100
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] Surface Tension of a lipid bilayer
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <457145CD.7010602 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>toma0052 wrote:
> > Hello,
> > I have a question about calculating the surface tension for the
> > water-lipid interface of a lipid bilayer. After an MD run, I can
> use my .edr
> > file and g_energy to calculate the surface tension. I believe that the
> > surface tension is calculated something like gamma =
> (Pzz-(Pxx+Pyy)/2)/L. I
> > was wondering though, is the pressure tensor and hence surface tension
> > calculated over the entire simulation box? I would assume so, since I did
> > not specify any molecules. To find the water-lipid surface
> tension, would I
> > not need to sum over only the molecules at the surface? Would this be
> > do-able in Gromacs? Would I have to write something separate to do this?
> > In my coordinate file, I have DPPC atoms, solvent atoms, and
> other atoms
> > (those that make up the head group ie O,N etc.). Could I just
> make an index
> > group that is not DPPC and not Solvent, and sum over those atoms?
> >
> > Thanks,
> > Mike Tomasini
>First, one usually has two interfaces, in which case you have to divide
>the surface tension by two. This is computed over the entire box but it
>will give you a perfectly good result.
>
>Further it would be interesting to calculate local pressures, and there
>is an ancient gromacs version that does this (can be downloaded from the
>website). The reason this is not in standard gromacs is that it is quite
>expensive to compute.
>
>--
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>phone: 46 18 471 4205 fax: 46 18 511 755
>spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>------------------------------
>
>Message: 7
>Date: Sat, 02 Dec 2006 10:25:03 +0100
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] Segmentaion fault error- installing
> gromacs-3.3.1 on MacOSX
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4571466F.4010608 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>Ibrahim M. Moustafa wrote:
> > Hi gmx-users,
> >
> > I have a little problem with gromacs-3.3.1 installed on a Mac-OSX.
> > After installation (either building the package myself as instructed, or
> > using a binary form GROMACS web site) I could not run any program with
> > just typing the name on the xterm!
> > for example, issuing "pdb2gmx" command line gives an error message
> > "segmentation fault". However, typing the whole path name
> > "$GMXBIN/pdb2gmx or any other modules " works fine.
> > The variables for GROMACS are configured after the installation. My
> > .cshrc sources from the GMXRC.csh and the variables are defined; the
> > PATH includes the $GMXBIN also.
> > For the moment, I'm using alias to define the whole path for GROMACS
> > programs to run; though, this a bit annoying.
> >
> > I posted this problem in CCL and M.L. Dodson, replied with some
> > explanation for this weird problem:
> >
> > " Ahh... Think I have it. Looking at the source code on my BSD Unix
> > box, I see in src/gmxlib/copyrite.c the following:
> >
> > void CopyRight(FILE *out,char *szProgram)
> > {
> > /* Dont change szProgram arbitrarily - it must be argv[0], i.e. the
> > * name of a file. Otherwise, we won't be able to find the library dir.
> > */
> > #define NCR (int)asize(CopyrightText)
> > #define NGPL (int)asize(GPLText)
> >
> > char buf[256],tmpstr[1024];
> >
> > char *ptr;
> >
> > int i;
> >
> > set_program_name(szProgram);
> > .
> > .
> > .
> >
> > So I was right, it does use argv[0] for something: finding its
> > library directory."
> >
> > I wonder if there is a quick fix for this in the code, so I can run
> > the programs by just typing the name without need for the whole path!
> >
> > A question here: if Dodson is right, why the programer wrote the code
> > this way! is there any advantage?
> >
> > P.S. I have no previous experience with GROMACS
> >
> > thanks,
> > Ibrahim
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > 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
>Have you tried
>source $GMXBIN/GMXRC
>It will set up the necessary environment variables after which you can
>run it as usual (I do it all the time on my Macs).
>
>The advantage with this code is that you should be able to move the
>entire gromacs installation somewhere else.
>
>--
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>phone: 46 18 471 4205 fax: 46 18 511 755
>spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>------------------------------
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>
>
>End of gmx-users Digest, Vol 32, Issue 4
>****************************************
More information about the gromacs.org_gmx-users
mailing list