Dear Tamas and Mark, Thank you for your help. Since I am using GROMACS 4.6.x and 5, the default binary names are different, i.e., g_xxx versus gmx xxx, compiling with different suffixes are not necessary. It seems Mark's idea is most fault-proof, though sourcing different .bashrc files one at a time defeats the my purpose of asking this question. Thank you guys anyway.
Regards, Bin 2014-08-04 9:52 GMT-04:00 <[email protected] >: > Send gromacs.org_gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: Any way to use GROMACS 4.6.x and 5 together (Tamas Karpati) > 2. Error in inflategro.pl (neha bharti) > 3. Re: Any way to use GROMACS 4.6.x and 5 together (Mark Abraham) > 4. Re: Any way to use GROMACS 4.6.x and 5 together (Tamas Karpati) > 5. Re: Error with tabulated potential and tip4p water model > (Udaya Dahal) > 6. Re: Output help (Victor Rosas Garcia) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 4 Aug 2014 13:08:00 +0200 > From: Tamas Karpati <[email protected]> > To: [email protected] > Subject: Re: [gmx-users] Any way to use GROMACS 4.6.x and 5 together > Message-ID: > < > can5ox5p7mwbsir+jos13vux3pe_4xfkfoksutzdc8rmbncx...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Dear Bin, > > On Sat, Aug 2, 2014 at 12:44 PM, massimo sandal <[email protected]> > wrote: > > Compile them with different suffixes? So that you have binaries like > > mdrun_46 and mdrun_50 ? > > Additional tip: if you don't want to rename all the executables > you may simply create a soft link to one of the install folders, > then -when need to change- remove it then re-create with the other one. > > In detail: I have the following lines in my /home/myname/.bashrc: > > export PATH=${PATH}:${HOME}/gromacs_bin/bin > export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/gromacs_bin/lib > > I have two (in fact more) compiled versions: gromacs-4.6.6_bin and > gromacs-5.0_bin. When I want to use the 4.6.6 version: > > rm -f ~/gromacs_bin > ln -s ~/gromacs-4.6.6_bin ~/gromacs_bin > > Then to switch to the other: > > rm -f ~/gromacs_bin > ln -s ~/gromacs-5.0_bin ~/gromacs_bin > > If you're in a unix shell, you need to re-open it for .bashrc to take > effect. > > I assumed you're running GROMACS under some Linux/Unix platform > but probably the same can be achieved on any other OS. > > Hope this helps, > t > > > On 2 Aug 2014 00:32, "Bin Liu" <[email protected]> wrote: > > > >> Dear everyone, > >> > >> I am having trouble with putting GROMACS 4.6.x and 5 together. If I put > >> these two lines in .bashrc file, > >> > >> source /usr/local/gromacs4.6.5/bin/GMXRC > >> source /usr/local/gromacs5.0/bin/GMXRC > >> > >> The second line will undo the work by the first line, i.e., I can use > only > >> gmx order of GROMACS 5 (for example), not g_order of GROMACS 4.6.5 > >> > >> Is there any way to let these two versions work together? Or I should > just > >> put both directories in the PATH environment variable? Thanks. > >> > >> Cheers, > >> > >> Bin > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to [email protected]. > >> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > > > ------------------------------ > > Message: 2 > Date: Mon, 4 Aug 2014 17:00:10 +0530 > From: neha bharti <[email protected]> > To: [email protected] > Subject: [gmx-users] Error in inflategro.pl > Message-ID: > < > cajtvtjcqwhbc_s_npbkgv8q6y3mfkhuw2u7fokpy4bprzpb...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hello All > > I am trying to perform MD for protein ligand protein complex in popc lipid > with charmm36 force field and also follow Justin A. Lemkul tutorial. > > I generated small molecule topology file from SwissParam which provides > .pdb file for ligand molecule. > I don't have .gro file for small molecule thats why I have created all the > file in .pdb file format. > > when I run: > > perl inflategro.pl system.pdb 4 POPC 0 system_inflated.gro 5 area.dat > > it gives error : > > Use of uninitialized value $box_x in multiplication (*) at inflategro.pl > line 339. > Use of uninitialized value $box_y in multiplication (*) at inflategro.pl > line 340. > Scaling lipids.... > There are 0 lipids... > > > How to work with .pdb file to run inflategro.pl command?? > > can anyone please help me out how to solve this error. > > Thanks in advance > > Neha bharti > > > ------------------------------ > > Message: 3 > Date: Mon, 4 Aug 2014 07:39:05 -0400 > From: Mark Abraham <[email protected]> > To: Discussion list for GROMACS users <[email protected]> > Subject: Re: [gmx-users] Any way to use GROMACS 4.6.x and 5 together > Message-ID: > < > camnumat2y+lmc9x6_ju-zru1fwl8xo5yxcm5gr0j6akeb4r...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Just sourcing the corresponding GMXRC when you want to switch is a quicker > and easier solution! > > Mark > > > On Mon, Aug 4, 2014 at 7:08 AM, Tamas Karpati <[email protected]> wrote: > > > Dear Bin, > > > > On Sat, Aug 2, 2014 at 12:44 PM, massimo sandal <[email protected]> > > wrote: > > > Compile them with different suffixes? So that you have binaries like > > > mdrun_46 and mdrun_50 ? > > > > Additional tip: if you don't want to rename all the executables > > you may simply create a soft link to one of the install folders, > > then -when need to change- remove it then re-create with the other one. > > > > In detail: I have the following lines in my /home/myname/.bashrc: > > > > export PATH=${PATH}:${HOME}/gromacs_bin/bin > > export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/gromacs_bin/lib > > > > I have two (in fact more) compiled versions: gromacs-4.6.6_bin and > > gromacs-5.0_bin. When I want to use the 4.6.6 version: > > > > rm -f ~/gromacs_bin > > ln -s ~/gromacs-4.6.6_bin ~/gromacs_bin > > > > Then to switch to the other: > > > > rm -f ~/gromacs_bin > > ln -s ~/gromacs-5.0_bin ~/gromacs_bin > > > > If you're in a unix shell, you need to re-open it for .bashrc to take > > effect. > > > > I assumed you're running GROMACS under some Linux/Unix platform > > but probably the same can be achieved on any other OS. > > > > Hope this helps, > > t > > > > > On 2 Aug 2014 00:32, "Bin Liu" <[email protected]> wrote: > > > > > >> Dear everyone, > > >> > > >> I am having trouble with putting GROMACS 4.6.x and 5 together. If I > put > > >> these two lines in .bashrc file, > > >> > > >> source /usr/local/gromacs4.6.5/bin/GMXRC > > >> source /usr/local/gromacs5.0/bin/GMXRC > > >> > > >> The second line will undo the work by the first line, i.e., I can use > > only > > >> gmx order of GROMACS 5 (for example), not g_order of GROMACS 4.6.5 > > >> > > >> Is there any way to let these two versions work together? Or I should > > just > > >> put both directories in the PATH environment variable? Thanks. > > >> > > >> Cheers, > > >> > > >> Bin > > >> -- > > >> Gromacs Users mailing list > > >> > > >> * Please search the archive at > > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > >> posting! > > >> > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > >> * For (un)subscribe requests visit > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > >> send a mail to [email protected]. > > >> > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > > > > > ------------------------------ > > Message: 4 > Date: Mon, 4 Aug 2014 13:48:36 +0200 > From: Tamas Karpati <[email protected]> > To: [email protected] > Subject: Re: [gmx-users] Any way to use GROMACS 4.6.x and 5 together > Message-ID: > < > can5ox5ntpw7zdowgmz1pwm8jhw_qs4akhhstcz0w0buz3mv...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Dear Mark, > > Somehow I felt that I should have read the Manual.... thanks :) > > Bin, pelase forget my post. > t > > > On Mon, Aug 4, 2014 at 1:39 PM, Mark Abraham <[email protected]> > wrote: > > Just sourcing the corresponding GMXRC when you want to switch is a > quicker > > and easier solution! > > > > Mark > > > > > > On Mon, Aug 4, 2014 at 7:08 AM, Tamas Karpati <[email protected]> > wrote: > > > >> Dear Bin, > >> > >> On Sat, Aug 2, 2014 at 12:44 PM, massimo sandal <[email protected] > > > >> wrote: > >> > Compile them with different suffixes? So that you have binaries like > >> > mdrun_46 and mdrun_50 ? > >> > >> Additional tip: if you don't want to rename all the executables > >> you may simply create a soft link to one of the install folders, > >> then -when need to change- remove it then re-create with the other one. > >> > >> In detail: I have the following lines in my /home/myname/.bashrc: > >> > >> export PATH=${PATH}:${HOME}/gromacs_bin/bin > >> export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/gromacs_bin/lib > >> > >> I have two (in fact more) compiled versions: gromacs-4.6.6_bin and > >> gromacs-5.0_bin. When I want to use the 4.6.6 version: > >> > >> rm -f ~/gromacs_bin > >> ln -s ~/gromacs-4.6.6_bin ~/gromacs_bin > >> > >> Then to switch to the other: > >> > >> rm -f ~/gromacs_bin > >> ln -s ~/gromacs-5.0_bin ~/gromacs_bin > >> > >> If you're in a unix shell, you need to re-open it for .bashrc to take > >> effect. > >> > >> I assumed you're running GROMACS under some Linux/Unix platform > >> but probably the same can be achieved on any other OS. > >> > >> Hope this helps, > >> t > >> > >> > On 2 Aug 2014 00:32, "Bin Liu" <[email protected]> wrote: > >> > > >> >> Dear everyone, > >> >> > >> >> I am having trouble with putting GROMACS 4.6.x and 5 together. If I > put > >> >> these two lines in .bashrc file, > >> >> > >> >> source /usr/local/gromacs4.6.5/bin/GMXRC > >> >> source /usr/local/gromacs5.0/bin/GMXRC > >> >> > >> >> The second line will undo the work by the first line, i.e., I can use > >> only > >> >> gmx order of GROMACS 5 (for example), not g_order of GROMACS 4.6.5 > >> >> > >> >> Is there any way to let these two versions work together? Or I should > >> just > >> >> put both directories in the PATH environment variable? Thanks. > >> >> > >> >> Cheers, > >> >> > >> >> Bin > >> >> -- > >> >> Gromacs Users mailing list > >> >> > >> >> * Please search the archive at > >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> >> posting! > >> >> > >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> >> > >> >> * For (un)subscribe requests visit > >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > >> >> send a mail to [email protected]. > >> >> > >> > -- > >> > Gromacs Users mailing list > >> > > >> > * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > >> > * For (un)subscribe requests visit > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to [email protected]. > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to [email protected]. > >> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > > > ------------------------------ > > Message: 5 > Date: Mon, 4 Aug 2014 09:48:23 -0400 > From: Udaya Dahal <[email protected]> > To: [email protected] > Subject: Re: [gmx-users] Error with tabulated potential and tip4p > water model > Message-ID: > < > cag1jmthlhc_hvt98xnq9a3rh3erqzxoyvksakn1+xfszyd7...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > It was immediate. But I figured out the way to solve that issue. Looks > like the starting initial configuration was not so good. A different > starting structure at least gave me the energy minimization to few steps > but I kind of really find very hard to have the energy minimized to smaller > value. The maximum force on the particular atom is around ...+03. Do I > really have to amend each and every atom step by step(which still doesn't > solve the problem) or there is any other specific way that we can get > more/less energy minimized structure. Thank you for your help. > > > On Sun, Aug 3, 2014 at 9:23 PM, Mark Abraham <[email protected]> > wrote: > > > Immediately, or after some EM steps? > > > > Mark > > > > > > On Sun, Aug 3, 2014 at 12:56 PM, Udaya Dahal <[email protected]> > > wrote: > > > > > I have tabulated potential for all the possible combinations(non > > bonded). > > > I am using Tip4p water model for the polymer water interaction. While > > > running the energy minimization i got the error like below. > > > > > > Fatal error: > > > Settle block crossing node boundaries > > > constraint between atoms 664, 665, 666) > > > For more information and tips for troubleshooting, please check the > > GROMACS > > > website at http://www.gromacs.org/Documentation/Errors > > > > > > Any idea to slove this issue.? > > > > > > Thank you, > > > Udaya. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to [email protected]. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > > > > > > -- > Udaya Dahal, > Graduate Assistant, > Department of Physics, > University of Connecticut > > > ------------------------------ > > Message: 6 > Date: Mon, 4 Aug 2014 08:52:29 -0500 > From: Victor Rosas Garcia <[email protected]> > To: [email protected] > Subject: Re: [gmx-users] Output help > Message-ID: > < > cajota7brpgjsukxg5ffb6a25u9nkw1tpsxbamjt4gpmnpbt...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > If you are under Linux, you could use "tail" to get rid of the lines > you don't want. Check "man tail" for details. > > Hope this helps > > Victor > > 2014-08-03 17:57 GMT-05:00 Marco Rougeth <[email protected]>: > > Hello! > > > > I using grompp and mdrun and the output text shows too much text, like > the > > version, contributors names, copyright and all the options used. How can > I > > omit all of them? I tried to redirect the output, but it did not worked. > > > > Thank you! > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > > > End of gromacs.org_gmx-users Digest, Vol 124, Issue 10 > ****************************************************** > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
