Thank Roland very much. I have read it and I understood it a litle. Wishing all good things come to you
Man Hoang Viet > 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. regarding dimethylated lysine topology file (prasun kumar) > 2. Re: How to define protein surface residues (Lee Soin) > 3. about LINCS WARNING (mhv...@ifpan.edu.pl) > 4. Re: about LINCS WARNING (Roland Schulz) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 3 Mar 2009 03:06:17 -0800 > From: prasun kumar <prasu...@gmail.com> > Subject: [gmx-users] regarding dimethylated lysine topology file > To: gmx-users@gromacs.org > Message-ID: > <a473abdb0903030306x1c8ef034gfad6f5b0dcb89...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Respected all > I drew the structure using the drawing tool available in PRODRG server > then I went for topology file generation,but the server is deleting > almost > all the hydrogen atoms while writing the topology file for gromacs > can any one tell me why it is doing like this? > > another question I got that is > how to change gromacs topology file to charmm topology file > (I know for bond length and angle........but for dihedral(improper and > proper)) > actually i want toi know which function gromacs is using for the > calculation > of dihedrals.......... > thanx in advance > > PRASUN (ASHOKA) > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090303/a41dfb5d/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Tue, 3 Mar 2009 19:09:20 +0800 > From: Lee Soin <nomad...@gmail.com> > Subject: Re: [gmx-users] How to define protein surface residues > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <e2838e4e0903030309v5aa07d8y1732299774bbe...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Thanks, but what I mean is to just find out the surface residues, not to > calculate the surface area. > > 2009/3/3 David van der Spoel <sp...@xray.bmc.uu.se> > >> Lee Soin wrote: >> >>> Hello! >>> I'm trying to find the surface residues of a protein. Maybe this should >>> be >>> calculated by myself and not using GROMACS. Can anybody tell me a >>> feasible >>> procedure for doing so? Thanks! >>> >> g_sas >> >> -- >>> Sun Li >>> Department of Physics >>> Nanjing University, China >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> 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 >>> >> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. >> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >> _______________________________________________ >> 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 >> > > > > -- > Sun Li > Department of Physics > Nanjing University, China > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090303/4ddc0177/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Tue, 3 Mar 2009 12:19:45 +0100 (CET) > From: mhv...@ifpan.edu.pl > Subject: [gmx-users] about LINCS WARNING > To: gmx-users@gromacs.org > Message-ID: > <a06ae90e88c90feef7e6c9a8948997ee.squir...@webmail.ifpan.edu.pl> > Content-Type: text/plain;charset=iso-8859-1 > > Thank David very much > I have tried and most of them work. > And, When I run script_mini.mdp to minimize energy and it report LINCS > warning (as below). So Can you tell me What LINCS WARNING mean? > > Step 16, time 0.032 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.000000, max 0.000001 (between atoms 18 and 20) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 97 98 35.3 0.1000 0.1000 0.1000 > > > >> 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. Detail of Script.sh in Gromacs-4.0.3? (mhv...@ifpan.edu.pl) >> 2. Re: How to define protein surface residues (David van der Spoel) >> 3. Re: Detail of Script.sh in Gromacs-4.0.3? (David van der Spoel) >> 4. SV: SV: [gmx-users] g_order version 4.0.x (Sarah Witzke) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 3 Mar 2009 10:37:05 +0100 (CET) >> From: mhv...@ifpan.edu.pl >> Subject: [gmx-users] Detail of Script.sh in Gromacs-4.0.3? >> To: gmx-users@gromacs.org >> Message-ID: >> <24e6018b503b7a1516fccea3477b4d8d.squir...@webmail.ifpan.edu.pl> >> Content-Type: text/plain;charset=iso-8859-1 >> >> Dear all >> >> I am newer in Gromacs. Now I am studying Gomacs for protein simulations. >> I >> am trying script files which used for gromacs-3. Can I do it? Does >> Gromacs-4. have to use others script files? and If It have, Can you send >> sript files to me for gromacs-4? >> Thank you verry much! >> >> Yours truly, >> >> Man Hoang Viet >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Tue, 03 Mar 2009 10:52:07 +0100 >> From: David van der Spoel <sp...@xray.bmc.uu.se> >> Subject: Re: [gmx-users] How to define protein surface residues >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Message-ID: <49acfdc7.6060...@xray.bmc.uu.se> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Lee Soin wrote: >>> Hello! >>> I'm trying to find the surface residues of a protein. Maybe this should >>> be calculated by myself and not using GROMACS. Can anybody tell me a >>> feasible procedure for doing so? Thanks! >>> >> g_sas >> >>> -- >>> Sun Li >>> Department of Physics >>> Nanjing University, China >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> 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 >> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. >> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >> >> >> ------------------------------ >> >> Message: 3 >> Date: Tue, 03 Mar 2009 10:54:42 +0100 >> From: David van der Spoel <sp...@xray.bmc.uu.se> >> Subject: Re: [gmx-users] Detail of Script.sh in Gromacs-4.0.3? >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Message-ID: <49acfe62.6030...@xray.bmc.uu.se> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> mhv...@ifpan.edu.pl wrote: >>> Dear all >>> >>> I am newer in Gromacs. Now I am studying Gomacs for protein >>> simulations. >>> I >>> am trying script files which used for gromacs-3. Can I do it? Does >>> Gromacs-4. have to use others script files? and If It have, Can you >>> send >>> sript files to me for gromacs-4? >>> Thank you verry much! >> >> Have you tried? >> >> Most of them will work. >> >>> >>> Yours truly, >>> >>> Man Hoang Viet >>> >>> _______________________________________________ >>> 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 >> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. >> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >> >> >> ------------------------------ >> >> Message: 4 >> Date: Tue, 3 Mar 2009 11:37:56 +0100 >> From: "Sarah Witzke" <sawi...@student.sdu.dk> >> Subject: SV: SV: [gmx-users] g_order version 4.0.x >> To: <jalem...@vt.edu>, "Discussion list for GROMACS users" >> <gmx-users@gromacs.org> >> Message-ID: >> <3bc166246158f845a8abbaca9eee1e2d09147...@adm-exch0c.adm.c.sdu.dk> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Good idea, I'll try that when I get home next week. >> >> -Sarah >> >> ________________________________ >> >> Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul >> Sendt: ma 02-03-2009 13:58 >> Til: Discussion list for GROMACS users >> Emne: Re: SV: [gmx-users] g_order version 4.0.x >> >> >> >> >> >> Sarah Witzke wrote: >>> Thank you David, I have filled a bugzilla. >>> >> >> g_order works for me under version 4.0.4, perhaps try an upgrade? >> >> -Justin >> >> ________________________________ >>> >>> Fra: gmx-users-boun...@gromacs.org på vegne af David van der Spoel >>> Sendt: ma 02-03-2009 10:55 >>> Til: Discussion list for GROMACS users >>> Emne: Re: [gmx-users] g_order version 4.0.x >>> >>> >>> >>> Sarah Witzke wrote: >>>> Dear Gromacs users, >>>> >>>> >>>> >>>> I'm sorry to resend this email but I sent it yesterday (27 hours ago) >>>> and I still haven't received it myself. I'm sorry for the >>>> inconvenience >>>> it might cause. >>>> >>>> >>>> >>>> Sarah >>>> >>>> >>>> ________________________________ >>>> >>>> Dear Gromacs Users, >>>> >>>> >>>> >>>> I have simulated a lipid bilayer (128 DMPC molecules) with some small >>>> hydrophobic molecules. These small molecules go from the water into >>>> the >>>> bilayer and I now want to do some analysis to see, whether this has >>>> changed e.g. membrane thickness or the order of the lipid tails. I'm >>>> new to gromacs and this is my first try with analysis. >>>> >>>> For analysing the order of the lipid tales, I use g_order. The first >>>> index file I created consisted of 28 groups - one for each of the 14 >>>> carbons (including the carbonyl-C) in the two chains. The atoms in >>>> each >>>> of the 128 lipid molecules have the same atom name (e.g. c1, c2...) so >>>> each of the 28 groups in the index file consist of 128 atoms (an entry >>>> in make_ndx would look like this "a c15 & r DMPC"). >>>> >>>> Then I tried g_order version 4.0.2: >>>> >>>> >>>> >>>> g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b >>>> 100000 -od dmpclim3_order_2.xvg >>>> >>>> >>>> >>>> I'm asked to "Select the group that contains the atoms you want to use >>>> for the tetrahedrality order parameter calculation:" and then all the >>>> 28 groups are listed. This was not what I had expected; I thought >>>> g_order calculated the order parameter for all the tail carbons at >>>> once. I tried just choosing group 0 to see what happened: Not much - >>>> as >>>> was expected. Two files were generated: sg-ang.xvg and sk-dist.xvg. >>>> This I found strange since I hadn't asked for them, but then I found >>>> this bugzilla report: >>>> http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ >>>> <https://sdumail.sdu.dk/exchweb/bin/redir.asp?URL=http://www.gromacs.org/component/option,com_wrapper/Itemid,157/> >>>> (no. 264) >>>> >>>> >>>> >>>> >>>> >>>> After reading that I also tried to specify all carbons in one single >>>> group and then run g_order again: >>>> >>>> >>>> >>>> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b >>>> 100000 -od dmpclim3_order_2.xvg >>>> >>>> >>>> >>>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) >>>> >>>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) >>>> >>>> Select the group that contains the atoms you want to use for the >>>> tetrahedrality order parameter calculation: >>>> >>>> Group 0 >>>> (C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC) >>>> has 3584 elements >>>> >>>> There is one group in the index >>>> >>>> Reading frame 0 time 100000.008 >>>> >>>> Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1# >>>> >>>> >>>> >>>> Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1# >>>> >>>> Reading frame 11000 time 210000.016 >>>> >>>> >>>> >>>> Again I only got sg-ang.xvg and sk-dist.xvg but not the wanted >>>> deuterium order .xvg file. >>>> >>>> >>>> >>>> So, in the bugzilla report it also said that the problem had been >>>> fixed >>>> in the CVS. Unfortunately I don't know what this is, could anyone >>>> explain me please? >>>> >>>> >>>> >>>> I tried g_order version 4.0.3 (again with the index file with only one >>>> group): >>>> >>>> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b >>>> 100000 -od dmpclim3_order_3.xvg >>>> >>>> >>>> >>>> Taking z axis as normal to the membrane >>>> >>>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) >>>> >>>> Using following groups: >>>> >>>> Groupname: >>>> C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC >>>> First atomname: C15 First atomnr 44 >>>> >>>> >>>> >>>> Reading frame 0 time 100000.008 Number of elements in first >>>> group: 3584 >>>> >>>> Reading frame 11000 time 210000.016 >>>> >>>> >>>> >>>> Read trajectory. Printing parameters to file >>>> >>>> >>>> >>>> Now two order files are generated: The wanted dmpclim3_order_3.xvg and >>>> also order.xvg which I didn't request for. (No sg-ang.xvg and >>>> sk-dist.xvg this time). >>>> >>>> Unfortunately neither of the obtained .xvg files contain any order >>>> parameters: >>>> >>>> >>>> >>>> dmpclim3_order_3.xvg: >>>> >>>> # This file was created Sat Feb 28 20:02:09 2009 >>>> >>>> # by the following command: >>>> >>>> # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b >>>> 100000 -od dmpclim3_order_3.xvg >>>> >>>> # >>>> >>>> # g_order is part of G R O M A C S: >>>> >>>> # >>>> >>>> # Great Red Oystrich Makes All Chemists Sane >>>> >>>> # >>>> >>>> @ title "Deuterium order parameters" >>>> >>>> @ xaxis label "Atom" >>>> >>>> @ yaxis label "Scd" >>>> >>>> @TYPE xy >>>> >>>> >>>> >>>> order.xvg: >>>> >>>> # This file was created Sat Feb 28 20:02:09 2009 >>>> >>>> # by the following command: >>>> >>>> # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b >>>> 100000 -od dmpclim3_order_3.xvg >>>> >>>> # >>>> >>>> # g_order is part of G R O M A C S: >>>> >>>> # >>>> >>>> # Great Red Oystrich Makes All Chemists Sane >>>> >>>> # >>>> >>>> @ title "Order tensor diagonal elements" >>>> >>>> @ xaxis label "Atom" >>>> >>>> @ yaxis label "S" >>>> >>>> @TYPE xy >>>> >>>> >>>> >>>> I will be very thankful if anyone has any suggestions as to what I'm >>>> doing wrong? >>>> >>>> >>> Please submit a bugzilla. >>> I fixed something before 4.0.3, but apparently not everything. >>> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala >>> University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. >>> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >>> <http://folding.bmc.uu.se/> <http://folding.bmc.uu.se/> >>> _______________________________________________ >>> 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 >>> >>> >>> _______________________________________________ >>> 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 >>> >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Graduate Research Assistant >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> 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 >> >> >> >> >> ------------------------------ >> >> _______________________________________________ >> 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 59, Issue 12 >> ***************************************** >> > > > > > ------------------------------ > > Message: 4 > Date: Tue, 3 Mar 2009 06:36:02 -0500 > From: Roland Schulz <rol...@utk.edu> > Subject: Re: [gmx-users] about LINCS WARNING > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <c93c21390903030336l7133166dr4a662fb24547...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Are you sure you are actually doing minimization and not MD? Check the > integrator option in the mdp file. Also take a look at: > http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings > > Roland > > On Tue, Mar 3, 2009 at 6:19 AM, <mhv...@ifpan.edu.pl> wrote: > >> Thank David very much >> I have tried and most of them work. >> And, When I run script_mini.mdp to minimize energy and it report LINCS >> warning (as below). So Can you tell me What LINCS WARNING mean? >> >> Step 16, time 0.032 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.000000, max 0.000001 (between atoms 18 and 20) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 97 98 35.3 0.1000 0.1000 0.1000 >> >> >> >> > 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. Detail of Script.sh in Gromacs-4.0.3? (mhv...@ifpan.edu.pl) >> > 2. Re: How to define protein surface residues (David van der Spoel) >> > 3. Re: Detail of Script.sh in Gromacs-4.0.3? (David van der Spoel) >> > 4. SV: SV: [gmx-users] g_order version 4.0.x (Sarah Witzke) >> > >> > >> > ---------------------------------------------------------------------- >> > >> > Message: 1 >> > Date: Tue, 3 Mar 2009 10:37:05 +0100 (CET) >> > From: mhv...@ifpan.edu.pl >> > Subject: [gmx-users] Detail of Script.sh in Gromacs-4.0.3? >> > To: gmx-users@gromacs.org >> > Message-ID: >> > <24e6018b503b7a1516fccea3477b4d8d.squir...@webmail.ifpan.edu.pl> >> > Content-Type: text/plain;charset=iso-8859-1 >> > >> > Dear all >> > >> > I am newer in Gromacs. Now I am studying Gomacs for protein >> simulations. >> I >> > am trying script files which used for gromacs-3. Can I do it? Does >> > Gromacs-4. have to use others script files? and If It have, Can you >> send >> > sript files to me for gromacs-4? >> > Thank you verry much! >> > >> > Yours truly, >> > >> > Man Hoang Viet >> > >> > >> > >> > ------------------------------ >> > >> > Message: 2 >> > Date: Tue, 03 Mar 2009 10:52:07 +0100 >> > From: David van der Spoel <sp...@xray.bmc.uu.se> >> > Subject: Re: [gmx-users] How to define protein surface residues >> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> > Message-ID: <49acfdc7.6060...@xray.bmc.uu.se> >> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> > >> > Lee Soin wrote: >> >> Hello! >> >> I'm trying to find the surface residues of a protein. Maybe this >> should >> >> be calculated by myself and not using GROMACS. Can anybody tell me a >> >> feasible procedure for doing so? Thanks! >> >> >> > g_sas >> > >> >> -- >> >> Sun Li >> >> Department of Physics >> >> Nanjing University, China >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> >> 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 >> > >> > >> > -- >> > David van der Spoel, Ph.D., Professor of Biology >> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala >> University. >> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: >> +4618511755. >> > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >> > >> > >> > ------------------------------ >> > >> > Message: 3 >> > Date: Tue, 03 Mar 2009 10:54:42 +0100 >> > From: David van der Spoel <sp...@xray.bmc.uu.se> >> > Subject: Re: [gmx-users] Detail of Script.sh in Gromacs-4.0.3? >> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> > Message-ID: <49acfe62.6030...@xray.bmc.uu.se> >> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> > >> > mhv...@ifpan.edu.pl wrote: >> >> Dear all >> >> >> >> I am newer in Gromacs. Now I am studying Gomacs for protein >> simulations. >> >> I >> >> am trying script files which used for gromacs-3. Can I do it? Does >> >> Gromacs-4. have to use others script files? and If It have, Can you >> send >> >> sript files to me for gromacs-4? >> >> Thank you verry much! >> > >> > Have you tried? >> > >> > Most of them will work. >> > >> >> >> >> Yours truly, >> >> >> >> Man Hoang Viet >> >> >> >> _______________________________________________ >> >> 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 >> > >> > >> > -- >> > David van der Spoel, Ph.D., Professor of Biology >> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala >> University. >> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: >> +4618511755. >> > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >> > >> > >> > ------------------------------ >> > >> > Message: 4 >> > Date: Tue, 3 Mar 2009 11:37:56 +0100 >> > From: "Sarah Witzke" <sawi...@student.sdu.dk> >> > Subject: SV: SV: [gmx-users] g_order version 4.0.x >> > To: <jalem...@vt.edu>, "Discussion list for GROMACS users" >> > <gmx-users@gromacs.org> >> > Message-ID: >> > <3bc166246158f845a8abbaca9eee1e2d09147...@adm-exch0c.adm.c.sdu.dk> >> > Content-Type: text/plain; charset="iso-8859-1" >> > >> > Good idea, I'll try that when I get home next week. >> > >> > -Sarah >> > >> > ________________________________ >> > >> > Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul >> > Sendt: ma 02-03-2009 13:58 >> > Til: Discussion list for GROMACS users >> > Emne: Re: SV: [gmx-users] g_order version 4.0.x >> > >> > >> > >> > >> > >> > Sarah Witzke wrote: >> >> Thank you David, I have filled a bugzilla. >> >> >> > >> > g_order works for me under version 4.0.4, perhaps try an upgrade? >> > >> > -Justin >> > >> > ________________________________ >> >> >> >> Fra: gmx-users-boun...@gromacs.org på vegne af David van der Spoel >> >> Sendt: ma 02-03-2009 10:55 >> >> Til: Discussion list for GROMACS users >> >> Emne: Re: [gmx-users] g_order version 4.0.x >> >> >> >> >> >> >> >> Sarah Witzke wrote: >> >>> Dear Gromacs users, >> >>> >> >>> >> >>> >> >>> I'm sorry to resend this email but I sent it yesterday (27 hours >> ago) >> >>> and I still haven't received it myself. I'm sorry for the >> inconvenience >> >>> it might cause. >> >>> >> >>> >> >>> >> >>> Sarah >> >>> >> >>> >> >>> ________________________________ >> >>> >> >>> Dear Gromacs Users, >> >>> >> >>> >> >>> >> >>> I have simulated a lipid bilayer (128 DMPC molecules) with some >> small >> >>> hydrophobic molecules. These small molecules go from the water into >> the >> >>> bilayer and I now want to do some analysis to see, whether this has >> >>> changed e.g. membrane thickness or the order of the lipid tails. I'm >> >>> new to gromacs and this is my first try with analysis. >> >>> >> >>> For analysing the order of the lipid tales, I use g_order. The first >> >>> index file I created consisted of 28 groups - one for each of the 14 >> >>> carbons (including the carbonyl-C) in the two chains. The atoms in >> each >> >>> of the 128 lipid molecules have the same atom name (e.g. c1, c2...) >> so >> >>> each of the 28 groups in the index file consist of 128 atoms (an >> entry >> >>> in make_ndx would look like this "a c15 & r DMPC"). >> >>> >> >>> Then I tried g_order version 4.0.2: >> >>> >> >>> >> >>> >> >>> g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b >> >>> 100000 -od dmpclim3_order_2.xvg >> >>> >> >>> >> >>> >> >>> I'm asked to "Select the group that contains the atoms you want to >> use >> >>> for the tetrahedrality order parameter calculation:" and then all >> the >> >>> 28 groups are listed. This was not what I had expected; I thought >> >>> g_order calculated the order parameter for all the tail carbons at >> >>> once. I tried just choosing group 0 to see what happened: Not much - >> as >> >>> was expected. Two files were generated: sg-ang.xvg and sk-dist.xvg. >> >>> This I found strange since I hadn't asked for them, but then I found >> >>> this bugzilla report: >> >>> http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ >> >>> < >> https://sdumail.sdu.dk/exchweb/bin/redir.asp?URL=http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ >> > >> >>> (no. 264) >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> After reading that I also tried to specify all carbons in one single >> >>> group and then run g_order again: >> >>> >> >>> >> >>> >> >>> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b >> >>> 100000 -od dmpclim3_order_2.xvg >> >>> >> >>> >> >>> >> >>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) >> >>> >> >>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) >> >>> >> >>> Select the group that contains the atoms you want to use for the >> >>> tetrahedrality order parameter calculation: >> >>> >> >>> Group 0 >> >>> >> (C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC) >> >>> has 3584 elements >> >>> >> >>> There is one group in the index >> >>> >> >>> Reading frame 0 time 100000.008 >> >>> >> >>> Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1# >> >>> >> >>> >> >>> >> >>> Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1# >> >>> >> >>> Reading frame 11000 time 210000.016 >> >>> >> >>> >> >>> >> >>> Again I only got sg-ang.xvg and sk-dist.xvg but not the wanted >> >>> deuterium order .xvg file. >> >>> >> >>> >> >>> >> >>> So, in the bugzilla report it also said that the problem had been >> fixed >> >>> in the CVS. Unfortunately I don't know what this is, could anyone >> >>> explain me please? >> >>> >> >>> >> >>> >> >>> I tried g_order version 4.0.3 (again with the index file with only >> one >> >>> group): >> >>> >> >>> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b >> >>> 100000 -od dmpclim3_order_3.xvg >> >>> >> >>> >> >>> >> >>> Taking z axis as normal to the membrane >> >>> >> >>> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) >> >>> >> >>> Using following groups: >> >>> >> >>> Groupname: >> >>> >> C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC >> >>> First atomname: C15 First atomnr 44 >> >>> >> >>> >> >>> >> >>> Reading frame 0 time 100000.008 Number of elements in first >> >>> group: 3584 >> >>> >> >>> Reading frame 11000 time 210000.016 >> >>> >> >>> >> >>> >> >>> Read trajectory. Printing parameters to file >> >>> >> >>> >> >>> >> >>> Now two order files are generated: The wanted dmpclim3_order_3.xvg >> and >> >>> also order.xvg which I didn't request for. (No sg-ang.xvg and >> >>> sk-dist.xvg this time). >> >>> >> >>> Unfortunately neither of the obtained .xvg files contain any order >> >>> parameters: >> >>> >> >>> >> >>> >> >>> dmpclim3_order_3.xvg: >> >>> >> >>> # This file was created Sat Feb 28 20:02:09 2009 >> >>> >> >>> # by the following command: >> >>> >> >>> # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b >> >>> 100000 -od dmpclim3_order_3.xvg >> >>> >> >>> # >> >>> >> >>> # g_order is part of G R O M A C S: >> >>> >> >>> # >> >>> >> >>> # Great Red Oystrich Makes All Chemists Sane >> >>> >> >>> # >> >>> >> >>> @ title "Deuterium order parameters" >> >>> >> >>> @ xaxis label "Atom" >> >>> >> >>> @ yaxis label "Scd" >> >>> >> >>> @TYPE xy >> >>> >> >>> >> >>> >> >>> order.xvg: >> >>> >> >>> # This file was created Sat Feb 28 20:02:09 2009 >> >>> >> >>> # by the following command: >> >>> >> >>> # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b >> >>> 100000 -od dmpclim3_order_3.xvg >> >>> >> >>> # >> >>> >> >>> # g_order is part of G R O M A C S: >> >>> >> >>> # >> >>> >> >>> # Great Red Oystrich Makes All Chemists Sane >> >>> >> >>> # >> >>> >> >>> @ title "Order tensor diagonal elements" >> >>> >> >>> @ xaxis label "Atom" >> >>> >> >>> @ yaxis label "S" >> >>> >> >>> @TYPE xy >> >>> >> >>> >> >>> >> >>> I will be very thankful if anyone has any suggestions as to what I'm >> >>> doing wrong? >> >>> >> >>> >> >> Please submit a bugzilla. >> >> I fixed something before 4.0.3, but apparently not everything. >> >> >> >> -- >> >> David van der Spoel, Ph.D., Professor of Biology >> >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala >> University. >> >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: >> +4618511755. >> >> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >> >> <http://folding.bmc.uu.se/> <http://folding.bmc.uu.se/> >> >> _______________________________________________ >> >> 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 >> >> >> >> >> >> _______________________________________________ >> >> 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 >> >> >> > >> > -- >> > ======================================== >> > >> > Justin A. Lemkul >> > Graduate Research Assistant >> > Department of Biochemistry >> > Virginia Tech >> > Blacksburg, VA >> > jalemkul[at]vt.edu | (540) 231-9080 >> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> > >> > ======================================== >> > _______________________________________________ >> > 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 >> > >> > >> > >> > >> > ------------------------------ >> > >> > _______________________________________________ >> > 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 59, Issue 12 >> > ***************************************** >> > >> >> >> _______________________________________________ >> 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 >> > > > > -- > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > 865-241-1537, ORNL PO BOX 2008 MS6309 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090303/f2d1a504/attachment.html > > ------------------------------ > > _______________________________________________ > 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 59, Issue 13 > ***************************************** > _______________________________________________ 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. 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