OK I'll use bonds 6 instead. Although I understand what "constraints = all-bonds" means, I prefer to be sure : are bonds 6 indeed treated as constraints ? Then, there should be no difference at all with bonds 1, if I am right. By the way, is there a simple way to treat all bonds but one as constraints ?
Thanks, Michael BON -------- Message d'origine-------- De: [EMAIL PROTECTED] de la part de [EMAIL PROTECTED] Date: lun. 05/05/2008 16:03 À: [email protected] Objet : gmx-users Digest, Vol 49, Issue 19 Send gmx-users mailing list submissions to [email protected] 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 [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 gmx-users digest..." Today's Topics: 1. double sids error ? what ?! (BON Michael) 2. Re: Angle definition in g_hbond ... (Mark Abraham) 3. Re: Angle definition in g_hbond ... (David van der Spoel) 4. Re: double sids error ? what ?! (David van der Spoel) 5. Re: problem with simulation of phosphatidic acid, possibly in my topology? (himanshu khandelia) ---------------------------------------------------------------------- Message: 1 Date: Mon, 5 May 2008 14:53:43 +0200 From: "BON Michael" <[EMAIL PROTECTED]> Subject: [gmx-users] double sids error ? what ?! To: <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi all, I got a "double sids error" when using grompp. What does it mean in the first place ? Apparently, it has to do with Lincs making shake-blocks when using constraint = all-bonds. I am simulating two strands of RNA, defined in the same .top file as I want to add some distance restraint between the two strands. I add some dummy atoms on a strand, and the problem occurs when I define bonds (type 1) linking those dummy atoms to the second one (maybe the fact that it is the second strand is coincidental). The problem disappear when I define a bond type 6 instead, or when I use constraint=all-bonds. I may have done some mistakes in the definition of my topology, but I can't poin them because I don't understand what a double sids error is. Thanks for your help, Michael Bon -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 2788 bytes Desc: not available Url : http://www.gromacs.org/pipermail/gmx-users/attachments/20080505/0bcccb27/attachment-0001.bin ------------------------------ Message: 2 Date: Mon, 05 May 2008 23:46:01 +1000 From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Angle definition in g_hbond ... To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed sharada wrote: > dear gmx-users, > > I have a very fundamental query. I am trying to obtain the backbone > hydrogen bonds formed during a 15ns simulation of a 35 long protein. > When I do this by using g_hbond and selecting the Backbone groups, I am > getting no hydrogen bonds at all . However, when I plot the hydrogen > bonds for some of the structures picked up through the dynamics using > InsightII I am able to see the backbone HBs in almost all of them. > > This is the command I am using: > > g_hbond -f HBD1_15npep.trr -s HBD1_5mr_md.tpr -n HBD1_10n_nsl.ndx -num > hnum.xvg -g hb.log > > this is the output I obtain and the hb.log file is not created : > > Reading file HBD1_5mr_md.tpr, VERSION 3.3 (single precision) > Specify 2 groups to analyze: > Group 0 ( Protein) has 358 elements > Group 1 ( Protein-H) has 271 elements > Group 2 ( C-alpha) has 36 elements > Group 3 ( Backbone) has 108 elements > Group 4 ( MainChain) has 144 elements > Group 5 (MainChain+Cb) has 177 elements > Group 6 ( MainChain+H) has 181 elements > Group 7 ( SideChain) has 177 elements > Group 8 ( SideChain-H) has 126 elements > Group 9 ( Prot-Masses) has 358 elements > Select a group: 3 > Selected 4: 'Backbone' > Select a group: 3 > Selected 4: 'Backbone' > Calculating hydrogen bonds in Backbone (108 atoms) > Found 0 donors and 72 acceptors > No Donors found I haven't used this tool, but the problem looks like it is here. Are there any hydrogens in this group? Mark ------------------------------ Message: 3 Date: Mon, 05 May 2008 15:50:36 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Angle definition in g_hbond ... To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Mark Abraham wrote: > sharada wrote: >> dear gmx-users, >> >> I have a very fundamental query. I am trying to obtain the backbone >> hydrogen bonds formed during a 15ns simulation of a 35 long protein. >> When I do this by using g_hbond and selecting the Backbone groups, I >> am getting no hydrogen bonds at all . However, when I plot the >> hydrogen bonds for some of the structures picked up through the >> dynamics using InsightII I am able to see the backbone HBs in >> almost all of them. >> >> This is the command I am using: >> >> g_hbond -f HBD1_15npep.trr -s HBD1_5mr_md.tpr -n HBD1_10n_nsl.ndx >> -num hnum.xvg -g hb.log >> >> this is the output I obtain and the hb.log file is not created : >> >> Reading file HBD1_5mr_md.tpr, VERSION 3.3 (single precision) >> Specify 2 groups to analyze: >> Group 0 ( Protein) has 358 elements >> Group 1 ( Protein-H) has 271 elements >> Group 2 ( C-alpha) has 36 elements >> Group 3 ( Backbone) has 108 elements >> Group 4 ( MainChain) has 144 elements >> Group 5 (MainChain+Cb) has 177 elements >> Group 6 ( MainChain+H) has 181 elements >> Group 7 ( SideChain) has 177 elements >> Group 8 ( SideChain-H) has 126 elements >> Group 9 ( Prot-Masses) has 358 elements >> Select a group: 3 >> Selected 4: 'Backbone' >> Select a group: 3 >> Selected 4: 'Backbone' >> Calculating hydrogen bonds in Backbone (108 atoms) >> Found 0 donors and 72 acceptors >> No Donors found > > I haven't used this tool, but the problem looks like it is here. Are > there any hydrogens in this group? use 6 > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ------------------------------ Message: 4 Date: Mon, 05 May 2008 15:53:50 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] double sids error ? what ?! To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed BON Michael wrote: > > Hi all, > > I got a "double sids error" when using grompp. What does it mean in the first > place ? > > Apparently, it has to do with Lincs making shake-blocks when using constraint > = all-bonds. > I am simulating two strands of RNA, defined in the same .top file as I want > to add some distance restraint > between the two strands. I add some dummy atoms on a strand, and the problem > occurs when I define bonds (type 1) > linking those dummy atoms to the second one (maybe the fact that it is the > second strand is coincidental). The problem disappear when I define a bond > type 6 instead, or when I use constraint=all-bonds. > I may have done some mistakes in the definition of my topology, but I can't > poin them because I don't understand what a double sids error is. > sid = shake id it means one atom is in multiple shake blocks it should not happen, but hey, sometimes life is unfair. Anyway, I think bond type 6 is what you need to use in these kind of cases. > Thanks for your help, > > Michael Bon > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ------------------------------ Message: 5 Date: Mon, 5 May 2008 15:56:10 +0200 From: "himanshu khandelia" <[EMAIL PROTECTED]> Subject: [gmx-users] Re: problem with simulation of phosphatidic acid, possibly in my topology? To: "Discussion list for GROMACS users" <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 PS: My previous email was accidentally sent from the gmail account of my colleague, who uses the same workstation. My apologies. This is just a disclaimer on her behalf. On Mon, May 5, 2008 at 11:34 AM, himanshu khandelia <[EMAIL PROTECTED]> wrote: > Hi, > > I am trying to run a simulation of a POPC bilayer mixed with some > mono-anionic Phosphatidic acid (POPA) , where the choline group is > replaced by a hydrogen atom. However, the energy of my simulation box > diverges, and I am trying to fix the problem. I also tried running a > simulation of PA solvated in water and a single sodium ion, but even > that does not work. I will try to provide as much detail as possible, > I hope someone can help point out some obvious error which I have not > been able to debug over 3 days. In the simulation of a single PA > molecule in water, MDRUN keeps complaining that the distance between > atoms H1 and O4 is very high (> 4 nm or so). The problem probably lies > in my topology, possibly in the bonded interactions? > > Thank you very very much for all suggestions. > > The headgroup of phosphatidic acid in my topology looks something like this: > > H1 > | > (-) O4 O2 > \ / > P3 (+) > / \ > (-)O5 O6 > | > C7-----etc..... (rest of lipid) > > The same region in the POPC topology looks something like this: > > C6-----etc (choline group) > | > (-) O9 O7 > \ / > P8 (+) > / \ > (-)O10 O11 > | > C12---------etc .... (rest of lipid) > > > Thus, only one new atom type, a H-atom was introduced. I replaced the > C6 of POPC by H1 on POPA. O7, P8, O9 were replaced by O2, P3, O4 and > so on (so atom indices differ by a factor of 5) > > In the following, I have copy-pasted the topology of POPA and POPC for > the above regions. The topology for POPC is the one on Tieleman's > webpage, of course. My topology is directly derived from it. > > > ############################################################################################### > ###### FOR POPA ####### > [ atoms ] > ; nr type resnr residu atom cgnr charge mass > 1 LHO 1 PAPA H1 1 0.400 > 1.0080 ; this is the new atom type, I defined it in the lipid.itp file > and also described non-bonded interactions and pairtypes for this > atom. > 2 LOS 1 PAPA O2 1 -0.600 15.9994 ; > 3 LP 1 PAPA P3 1 1.500 30.9738 > 4 LOM 1 PAPA O4 1 -0.800 15.9994 > 5 LOM 1 PAPA O5 1 -0.800 15.9994 > 6 LOS 1 PAPA O6 1 -0.700 > 15.9994 ; qtot:-1 > 7 LC2 1 PAPA C7 2 0.400 14.0270 > > [bonds ] > ; ai aj funct > 1 2 1 0.10000E+00 0.31380E+06 > 2 3 1 0.16100E+00 0.25100E+06 > 3 4 1 0.14800E+00 0.37660E+06 > 3 5 1 0.14800E+00 0.37660E+06 > 3 6 1 0.16100E+00 0.25100E+06 > 6 7 1 0.14300E+00 0.25100E+06 > ....etc > [ pairs ] > ; ai aj funct > 1 4 1 > 1 5 1 > 1 6 1 > 2 7 1 > 3 8 1 > 4 7 1 > .... etc .... > > [ angles ] > ; ai aj ak funct > 1 2 3 1 0.10960E+03 0.39750E+03 > 2 3 4 1 0.10960E+03 0.39750E+03 > 2 3 5 1 0.10960E+03 0.39750E+03 > 2 3 6 1 0.10300E+03 0.39750E+03 > 3 6 7 1 0.12000E+03 0.39750E+03 > 4 3 5 1 0.12000E+03 0.58580E+03 > 4 3 6 1 0.10960E+03 0.39750E+03 > 5 3 6 1 0.10960E+03 0.39750E+03 > > [ dihedrals ] > ; ai aj ak al funct phi0 cp mult > 1 2 3 6 1 0.0 1.05 3 > 1 2 3 6 1 0.0 3.14 2 > 2 3 6 7 1 0.0 1.05 3 > 2 3 6 7 1 0.0 3.14 2 > > ##################################################################################### > > > ##################################################################################### > ###### FOR POPC ####### > > [ atoms ] > ; nr type resnr residu atom cgnr charge mass > > ; 1 to 5 are from the choline group > > 6 LC2 1 POPC C6 1 0.4000 > 14.0270 ; qtot:1.0 > 7 LOS 1 POPC O7 1 -0.800 > 15.9994 ; qtot:0.54 > 8 LP 1 POPC P8 1 1.700 > 30.9738 ; qtot:2.3 > 9 LOM 1 POPC O9 1 -0.800 > 15.9994 ; qtot:1.5 > 10 LOM 1 POPC O10 1 -0.800 > 15.9994 ; qtot:0.7 > 11 LOS 1 POPC O11 1 -0.700 15.9994 ; > qtot:0 > 12 LC2 1 POPC C12 2 0.400 > 14.0270 ; qtot:0.08 > > [ bonds ] > ; ai aj funct > 6 7 1 0.14300E+00 0.25100E+06 > 7 8 1 0.16100E+00 0.25100E+06 > 8 9 1 0.14800E+00 0.37660E+06 > 8 10 1 0.14800E+00 0.37660E+06 > 8 11 1 0.16100E+00 0.25100E+06 > 11 12 1 0.14300E+00 0.25100E+06 > > [ pairs ] > ; ai aj funct > 4 7 1 > 5 8 1 > 6 9 1 > 6 10 1 > 6 11 1 > 7 12 1 > > [ angles ] > ; ai aj ak funct > 6 7 8 1 0.12000E+03 0.39750E+03 > 7 8 9 1 0.10960E+03 0.39750E+03 > 7 8 10 1 0.10960E+03 0.39750E+03 > 7 8 11 1 0.10300E+03 0.39750E+03 > 8 11 12 1 0.12000E+03 0.39750E+03 > 9 8 10 1 0.12000E+03 0.58580E+03 > 9 8 11 1 0.10960E+03 0.39750E+03 > 10 8 11 1 0.10960E+03 0.39750E+03 > > > [ dihedrals ] > ; ai aj ak al funct phi0 cp mult > 6 7 8 11 1 0.0 1.05 3 > 6 7 8 11 1 0.0 3.14 2 > 7 8 11 12 1 0.0 1.05 3 > 7 8 11 12 1 0.0 3.14 2 > > ############################################################################################### > ------------------------------ _______________________________________________ gmx-users mailing list [email protected] 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 49, Issue 19 *****************************************
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