Hi Prof. Mark Abraham I recived a tutorial from you that in the tutorial 3th molecule was one and there is not some of the 3th molecules that distributed randomly.
I will be very thankful if you introduce to me a tutorial about my work. Thanks alot Maria On Mon, May 9, 2011 at 11:37 AM, <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://lists.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. regarding creating tabulated potentials (sreelakshmi ramesh) > 2. Re: Re: gmx-users Digest, Vol 85, Issue 61 (Mark Abraham) > 3. regarding nacl simulation in water using tabulated potentials > (sreelakshmi ramesh) > 4. Re: RE: gmx-users Digest, Vol 85, Issue 53 (Mark Abraham) > 5. Re: regarding nacl simulation in water using tabulated > potentials (Mark Abraham) > 6. Re: regarding nacl simulation in water using tabulated > potentials (sreelakshmi ramesh) > 7. Re: regarding nacl simulation in water using tabulated > potentials (Mark Abraham) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 May 2011 11:12:20 +0530 > From: sreelakshmi ramesh <sree.laks...@research.iiit.ac.in> > Subject: [gmx-users] regarding creating tabulated potentials > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <BANLkTimhMBkb0Ptt4wKCj_Dx=nbxwcq...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > dear gmx users, > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110509/245ab8d2/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Mon, 09 May 2011 15:45:41 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 85, Issue 61 > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dc77f85.8010...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 9/05/2011 3:40 PM, Maria Hamilton wrote: > > Hi Dallas > > Please do not respond to whole digests - it confuses the archive. Cut > out the relevant part and reply to it. Also, please choose a meaningful > subject line. > > > You said that > > "Easiest way is probably set up the appropriate sized box for molecule > > 2, randomly distributed molecule 3 in appropriate number through it > > (genbox), then solvate that box with molecule 2, then combine that box > > with solvated box containing molecule 1." > > > > How can I combine the two different box?Do you know any tutorial for > this? > > Yes, the one on "biphasic systems" that I suggested two days ago that > you search for :-) > > Mark > > > ------------------------------ > > Message: 3 > Date: Mon, 9 May 2011 11:16:59 +0530 > From: sreelakshmi ramesh <sree.laks...@research.iiit.ac.in> > Subject: [gmx-users] regarding nacl simulation in water using > tabulated potentials > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <BANLkTi=upi92tu6dnjxm7oc9xfuk4hj...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > dear gmx users, > i have to simulate nacl in water...the system is > acubic box with just one na adn one cl ion in tip3p water.i wanted to use a > buckingham potential for na adn cl interaction and lennard jones for water > -ion intercation.i really dont have any idea on how to do this.any help > will > be of great use for me... > > thanks and regards, > shree > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110509/c048df19/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Mon, 09 May 2011 15:47:55 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] RE: gmx-users Digest, Vol 85, Issue 53 > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dc7800b.2080...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 9/05/2011 9:10 AM, Ryan S Davis (rsdavis1) wrote: > > I am not sure if I replied to this thread correctly, but anyway. > > Please use a relevant subject line. > > > I tried the things you guys suggested, but I still cant get it to work. > > You were right $HOME does have a slash in front but I am not actually > using that variable, just used it in the mailing list for convience, sorry. > > Copy and paste of actual terminal sessions is always preferable. > Computers are literal, and troubleshooting things filtered through > people's heads usually wastes time. > > > I reinstalled the libraries, just to make sure everything went well. > > So, here is what happens when I list out the library tree from my home > directory and try to run the test code > > > > $ ls -R /home/rsdavis1/apps/xdrfile/ > > > > /home/rsdavis1/apps/xdrfile/: > > bin include lib > > > > /home/rsdavis1/apps/xdrfile/bin: > > trr2xtc > > > > /home/rsdavis1/apps/xdrfile/include: > > xdrfile > > > > /home/rsdavis1/apps/xdrfile/include/xdrfile: > > xdrfile.h xdrfile_trr.h xdrfile_xtc.h > > > > /home/rsdavis1/apps/xdrfile/lib: > > libxdrfile.a libxdrfile.la > > > > $ > > $ > > $ icpc -I/home/rsdavis1/apps/xdrfile/include/xdrfile/ > -L/home/rsdavis1/apps/xdrfile/lib/ test.cpp -lxdrfile > > > > /tmp/icpcUuD5jZ.o: In function `main': > > test.cpp:(.text+0x33): undefined reference to > `read_xtc_natoms(char*, int*)' > > $ > > That should work, so long as icpc doesn't need some weird invocation to > look for non-shared libraries. Try > > /home/rsdavis1/apps/xdrfile/lib/libxdrfile.a > > instead of -lxdrfile > > > Mark > > > ------------------------------ > > Message: 5 > Date: Mon, 09 May 2011 15:50:26 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] regarding nacl simulation in water using > tabulated potentials > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dc780a2.5010...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote: > > dear gmx users, > > i have to simulate nacl in water...the system > > is acubic box with just one na adn one cl ion in tip3p water.i wanted > > to use a buckingham potential for na adn cl interaction and lennard > > jones for water -ion intercation.i really dont have any idea on how to > > do this.any help will be of great use for me... > > Can't be done simply. You'd have to use non-bonded interaction tables > for the Na-Cl interaction with properly constructed energy groups. > Search the manual and webpage for details. > > Mark > > > ------------------------------ > > Message: 6 > Date: Mon, 9 May 2011 11:31:20 +0530 > From: sreelakshmi ramesh <sree.laks...@research.iiit.ac.in> > Subject: Re: [gmx-users] regarding nacl simulation in water using > tabulated potentials > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <banlktinfz7bgzo_rgtkgvstkd7gsg8f...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > i had followed the instructions in themnaual for ninbonded interactions adn > had created two tables one for nacl adn other table for water ion > interations...i wanted some information on how to use these tables for > starting thee simulation > > On Mon, May 9, 2011 at 11:20 AM, Mark Abraham <mark.abra...@anu.edu.au > >wrote: > > > On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote: > > > >> dear gmx users, > >> i have to simulate nacl in water...the system is > >> acubic box with just one na adn one cl ion in tip3p water.i wanted to > use a > >> buckingham potential for na adn cl interaction and lennard jones for > water > >> -ion intercation.i really dont have any idea on how to do this.any help > will > >> be of great use for me... > >> > > > > Can't be done simply. You'd have to use non-bonded interaction tables for > > the Na-Cl interaction with properly constructed energy groups. Search the > > manual and webpage for details. > > > > Mark > > -- > > gmx-users mailing list 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. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110509/82807731/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Mon, 09 May 2011 17:07:19 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] regarding nacl simulation in water using > tabulated potentials > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dc792a7.70...@anu.edu.au> > Content-Type: text/plain; charset="iso-8859-1" > > On 9/05/2011 4:01 PM, sreelakshmi ramesh wrote: > > i had followed the instructions in themnaual for ninbonded > > interactions adn had created two tables one for nacl adn other table > > for water ion interations... > > That's not "I really don't have any idea on how to do this". Please ask > the question you want answered, or you're wasting everyone's time. > > > i wanted some information on how to use these tables for starting thee > > simulation > > Sorry, that's too general. You might want help with a command line, or > setting up the .mdp, or something else. Please read 6.7 of the manual, > try things, and ask a focused question. > > Mark > > > On Mon, May 9, 2011 at 11:20 AM, Mark Abraham <mark.abra...@anu.edu.au > > <mailto:mark.abra...@anu.edu.au>> wrote: > > > > On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote: > > > > dear gmx users, > > i have to simulate nacl in water...the > > system is acubic box with just one na adn one cl ion in tip3p > > water.i wanted to use a buckingham potential for na adn cl > > interaction and lennard jones for water -ion intercation.i > > really dont have any idea on how to do this.any help will be > > of great use for me... > > > > > > Can't be done simply. You'd have to use non-bonded interaction > > tables for the Na-Cl interaction with properly constructed energy > > groups. Search the manual and webpage for details. > > > > Mark > > -- > > gmx-users mailing list gmx-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 > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110509/ebdfffc7/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > 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! > > End of gmx-users Digest, Vol 85, Issue 65 > ***************************************** >
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