On Thu, Jun 4, 2009 at 1:40 PM, rituraj purohit <riturajpuro...@gmail.com>wrote:
> Dear mark > Where i can get the file with permission. > I downloaded from http://swift.cmbi.kun.nl/gv/dssp/ > $chmod a+x <path to>/dssp Rituraj > > On 6/4/09, gmx-users-requ...@gromacs.org <gmx-users-requ...@gromacs.org> > wrote: > > Send gmx-users mailing list submissions to > > gmx-users@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-requ...@gromacs.org > > > > You can reach the person managing the list at > > gmx-users-ow...@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. Re: PME on BlueGene (Mark Abraham) > > 2. about PMF calculation (mirc...@sjtu.edu.cn) > > 3. Replacing the PRODRG charges (Lucio Ricardo Montero Valenzuela) > > 4. Re: Replacing the PRODRG charges (Mark Abraham) > > 5. how to include ionic strength (amri ta) > > 6. Re: how to include ionic strength (Mark Abraham) > > 7. DSSP problem (rituraj purohit) > > 8. Re: DSSP problem (Mark Abraham) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Thu, 04 Jun 2009 11:06:16 +1000 > > From: Mark Abraham <mark.abra...@anu.edu.au> > > Subject: Re: [gmx-users] PME on BlueGene > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: <4a271e08.2090...@anu.edu.au> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Jakob Wohlert wrote: > > > Mark Abraham wrote: > > >> Jakob Wohlert wrote: > > >>> Hi, > > >>> > > >>> I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the > > >>> configuration options from the wiki I have succeeded insofar that I > > >>> have a > > >>> working program as long as I don't use PME. > > >>> > > >>> I have tried many different variants of fftw - 2.1.5, 3.2.1, single > > >>> precision, double precision, different compiler optimizations and so > on, > > >>> but it all ends the same: mdrun getting stuck somewhere in the > > >>> initialization process. > > >>> > > >>> However, by using the built in fft library FFTPACK instead of FFTW, > PME > > >>> will work, but that is not really an alternative. > > >>> > > >>> In at least a few cases I have been able to pinpoint the location > > >>> where it > > >>> hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls > > >>> MPI_Sendrecv, but then nothing else happens as far as I can tell. > > >>> > > >>> I'm confused and I have sort of ran out of ideas right now. Has > anyone > > >>> else encountered a problem like this, or has anyone any suggestions > > >>> how to > > >>> proceed from here? > > > Thanks for your answer! > > > > > >> That looks to me like the separate PME nodes are dying through some > > >> linking problem and the problem is only manifest on node 0 when its > > >> sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this > when > > >> all the nodes die at the first point they refer to a symbol in the > FFT > > >> library. > > >> > > >> Otherwise, looking at warnings/errors from the linker will be > required. > > > Ok, can you be a little more specific? Do you mean when compiling > fftw, > > > gromacs or both? I'm not very experienced with these kind of things. > > > > GROMACS links with the FFTW library, so there ought to be warnings of > > potential problems at link time, i.e. the final stage of a GROMACS "make > > mdrun" (having started with a clean configuration, either freshly > > unpacked or after "make clean"). The last 100 or so lines of the output > > of "make mdrun" should have any relevant data. > > > > >> Are you compiling an FFT library version for the back end, or the > > >> front end? > > > I'm trying to get it to work on the back end, on the front end it > works > > > fine! (So, I have fftw libraries for both). > > > > My BG/L FFTW-3.2 configure line is > > > > ../configure --prefix /hpc/home/mja163/progs CC=blrts_xlc --host=powerpc > > --build=ppc64 CFLAGS=-qbgl -qarch=440d -qtune=440 -qnoautoconfig -O5 > > --disable-fortran --enable-float > > > > but you may need to tweak that for BG/P for all I know. Let me know > > when/if something works and I'll update the wiki. > > > > Mark > > > > > > ------------------------------ > > > > Message: 2 > > Date: Thu, 04 Jun 2009 13:56:51 +0800 > > From: mirc...@sjtu.edu.cn > > Subject: [gmx-users] about PMF calculation > > To: gmx-users@gromacs.org > > Message-ID: <20090604135651.2wdhcqo28csw8...@webmail1.sjtu.edu.cn> > > Content-Type: text/plain; charset=GB2312; DelSp="Yes"; > format="flowed" > > > > Dear All: > > > > I want to do some PMF (Potenial of Mean Force) calculation by > > AFM pulling method using the pull code to study the unbinding of a > > protein and a ligand. > > > > I want pull the ligand from its binding site and calculate the > > PMF of the procedure, does it possible? > > > > I have read the user manual about PMF calculation carefully, but > > still not clear how to do . Does anyone have any tutorial about how to > > do this kind of calculation or any published papers doing this things? > > anyhelp is greatly appreciate! > > > > > > Best Wishes > > R-X Gu > > > > > > > > ------------------------------ > > > > Message: 3 > > Date: Thu, 04 Jun 2009 01:24:32 -0500 > > From: Lucio Ricardo Montero Valenzuela <lucio...@ibt.unam.mx> > > Subject: [gmx-users] Replacing the PRODRG charges > > To: gmx-users@gromacs.org > > Message-ID: <1244096672.4a2768a0e4...@webmail.ibt.unam.mx> > > Content-Type: text/plain; charset=ISO-8859-1 > > > > I want to run a MD in an unparameterized molecule similar to adenine. I > can get > > the approximated parameters in PRODRG. But I have read that PRODRG not > always > > give the correct charge. Is it a good idea to replace that charges using > the > > charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, > GLYCAM and > > OPLS forcefields)?. Or will it be mixing forcefields?. > > > > Lucio Ricardo Montero Valenzuela > > Instituto de Biotecnologia, UNAM > > Departamento de Biologia Molecular de Plantas > > Av. Universidad 2001, Col. Chamilpa > > Cuernavaca 62210 > > Mexico > > > > ---------------------------------------------------------------- > > Este mensaje fue enviado desde el servidor Webmail del Instituto de > Biotecnologia. > > > > > > ------------------------------ > > > > Message: 4 > > Date: Thu, 04 Jun 2009 16:29:03 +1000 > > From: Mark Abraham <mark.abra...@anu.edu.au> > > Subject: Re: [gmx-users] Replacing the PRODRG charges > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: <4a2769af.6000...@anu.edu.au> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Lucio Ricardo Montero Valenzuela wrote: > > > I want to run a MD in an unparameterized molecule similar to adenine. > I can get > > > the approximated parameters in PRODRG. But I have read that PRODRG not > always > > > give the correct charge. Is it a good idea to replace that charges > using the > > > charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, > GLYCAM and > > > OPLS forcefields)?. Or will it be mixing forcefields?. > > > > That depends on your target forcefield for your MD. > > > > Mark > > > > > > ------------------------------ > > > > Message: 5 > > Date: Thu, 4 Jun 2009 12:27:00 +0530 (IST) > > From: amri ta <amrita0092...@yahoo.co.in> > > Subject: [gmx-users] how to include ionic strength > > To: gmx-users@gromacs.org > > Message-ID: <418624.33836...@web8708.mail.in.yahoo.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear gromacs users, > > > > I am simulating a protein which works in salt solution within cell. I > have to include 4M salt (say, NaCl) to the simulation box. How can i include > such ionic strength? Please outline me the procedure. > > > > Thanks in advance. > > Amrita Paul > > > > > > > > > > Cricket on your mind? Visit the ultimate cricket website. Enter > http://beta.cricket.yahoo.com > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090604/84086c55/attachment-0001.html > > > > ------------------------------ > > > > Message: 6 > > Date: Thu, 04 Jun 2009 17:09:35 +1000 > > From: Mark Abraham <mark.abra...@anu.edu.au> > > Subject: Re: [gmx-users] how to include ionic strength > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: <4a27732f.1020...@anu.edu.au> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > amri ta wrote: > > > Dear gromacs users, > > > > > > I am simulating a protein which works in salt solution within cell. I > > > have to include 4M salt (say, NaCl) to the simulation box. How can i > > > include such ionic strength? Please outline me the procedure. > > > > If you do some tutorial material, you will find out the procedure for > > adding ions. Finding out how many ions to add is for you to calculate > :-) > > > > Mark > > > > > > ------------------------------ > > > > Message: 7 > > Date: Thu, 4 Jun 2009 12:52:32 +0530 > > From: rituraj purohit <riturajpuro...@gmail.com> > > Subject: [gmx-users] DSSP problem > > To: gmx-users@gromacs.org > > Message-ID: > > <685cca3f0906040022j73103651p972ec3922736e...@mail.gmail.com> > > Content-Type: text/plain; charset=ISO-8859-1 > > > > Dear all > > I want ti install DSSP for visualization of secondary structure in > > gromacs analysis. > > I am doing following procedure.. > > Copy the executable "dsspcmbi" to /usr/bin or /usr/local/bin > > ln -s dsspcmbi dssp > > And running it for my Pdb like that.... > > dssp file.pdb file.dssp > > > > BUt I am getting error "Permission Denied" even i m super user for the > > machine (root). > > > > [r...@localhost ~]# dssp > > bash: /usr/local/bin/dssp: Permission denied > > [r...@localhost ~]# > > > > Plaese any body tell the solution for this problem... > > > > Regard > > Rituraj > > > > > > > > -- > > "The future belongs to those who believe in the beauty of their dreams." > > > > > > ------------------------------ > > > > Message: 8 > > Date: Thu, 04 Jun 2009 17:28:13 +1000 > > From: Mark Abraham <mark.abra...@anu.edu.au> > > Subject: Re: [gmx-users] DSSP problem > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: <4a27778d.1060...@anu.edu.au> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > rituraj purohit wrote: > > > Dear all > > > I want ti install DSSP for visualization of secondary structure in > > > gromacs analysis. > > > I am doing following procedure.. > > > Copy the executable "dsspcmbi" to /usr/bin or /usr/local/bin > > > ln -s dsspcmbi dssp > > > And running it for my Pdb like that.... > > > dssp file.pdb file.dssp > > > > > > BUt I am getting error "Permission Denied" even i m super user for the > > > machine (root). > > > > > > [r...@localhost ~]# dssp > > > bash: /usr/local/bin/dssp: Permission denied > > > [r...@localhost ~]# > > > > > > Plaese any body tell the solution for this problem... > > > > You may still need execute permissions on the original executable. You > > should not ever be running as root when not installing software or > > maintaining the system. > > > > Mark > > > > > > ------------------------------ > > > > _______________________________________________ > > gmx-users mailing list > > gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > > > End of gmx-users Digest, Vol 62, Issue 26 > > ***************************************** > > > > > -- > "The future belongs to those who believe in the beauty of their dreams." > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA
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