[gmx-users] RE : double sids error ? what ?!
BON Michael
michael.bon at cea.fr
Tue May 6 09:40:58 CEST 2008
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
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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" <michael.bon at cea.fr>
Subject: [gmx-users] double sids error ? what ?!
To: <gmx-users at gromacs.org>
Message-ID:
<92F41516EE90B540BC03B8C4613EF6B933CCA6 at DIODON.extra.cea.fr>
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
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Message: 2
Date: Mon, 05 May 2008 23:46:01 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Angle definition in g_hbond ...
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <481F0F99.4040207 at anu.edu.au>
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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 <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] Angle definition in g_hbond ...
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <481F10AC.7090902 at xray.bmc.uu.se>
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
> _______________________________________________
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--
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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
------------------------------
Message: 4
Date: Mon, 05 May 2008 15:53:50 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] double sids error ? what ?!
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <481F116E.8010006 at xray.bmc.uu.se>
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 gmx-users at 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-request at gromacs.org.
> 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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
------------------------------
Message: 5
Date: Mon, 5 May 2008 15:56:10 +0200
From: "himanshu khandelia" <hkhandelia at gmail.com>
Subject: [gmx-users] Re: problem with simulation of phosphatidic acid,
possibly in my topology?
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
<897c4ba20805050656r4fc8e44al8d3312efb2b5b5e3 at mail.gmail.com>
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
<hkhandelia at gmail.com> 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
> ###############################################################################################
>
------------------------------
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