[gmx-users] gromacs.org_gmx-users Digest, Vol 120, Issue 95
sunita gupta
sunita.bio at gmail.com
Tue Apr 22 13:18:30 CEST 2014
Hello,
Several time I have extended my jobs using the protocol you have mentioned
above. I always used to get my output appended to the previous one, which
never required any concatenation.
This time my aim was to extend the job using new.mdp files (as the previous
one contained simulated annealing protocols to reach 500K temp and the new
job to have trajectories at 500K only)
So, I used 1st protocol of Changing .mdp file given in
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations. grompp
-f new.mdp -c old.tpr -o new.tpr -t old.cpt and mdrun -s new.tpr
As, a result I got new files this time, creating backup files for the
previous ones. I renamed those backup files as old files and trying to
concatenate with the new ones. I have only one .cpt file now, as its backup
file was not created.
Please let me know, If I am wrong or any alternate way to do this.
Regards
On Tue, Apr 22, 2014 at 3:24 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Cannot write trajectory frame; maybe you are out of disk
> space (Andrew Bostick)
> 2. Re: Fwd: Concatenating two trajectories (Sunita)
> 3. No default U-B types (Shima Arasteh)
> 4. Re: Fwd: Concatenating two trajectories (Venkat Reddy)
> 5. deprecating the Nabble forums (Rossen Apostolov)
> 6. Re: negative HB lifetime (Erik Marklund)
> 7. Re: No default U-B types (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 21 Apr 2014 19:30:32 -0700
> From: Andrew Bostick <andrew.bostick1 at gmail.com>
> To: gmx-users <gmx-users at gromacs.org>
> Subject: [gmx-users] Cannot write trajectory frame; maybe you are out
> of disk space
> Message-ID:
> <
> CAMgMS2WLi3DHLUMhw_Erpy5TMffEBcyHqenoLy340nOJm1q7eA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Mark
>
> Thanks for your reply.
>
> I googled file permission in linux OS. After that I did following steps:
>
> I created a directory entitled input.
>
> I put pdb and mdp files in the input directory.
>
> I used following command to change permission:
>
> chmod -R 777 input
>
> Now I will md simulation steps (pdb2gmx .... editconf ..........)
>
> Is my manner true?
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 21 Apr 2014 22:30:00 -0700 (PDT)
> From: Sunita <sunita.bio at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Fwd: Concatenating two trajectories
> Message-ID: <1398144600309-5015992.post at n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hello Venkat,
>
> Yeah, I think by default it will give 0 ps as start time for both
> trajectories and it should be set by user using -settime flag
> Correct me if I am wrong.
>
> Regards
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Fwd-Concatenating-two-trajectories-tp5015956p5015992.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 21 Apr 2014 23:31:55 -0700 (PDT)
> From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
> To: Discussion List for GROMACS Users <gmx-users at gromacs.org>
> Subject: [gmx-users] No default U-B types
> Message-ID:
> <1398148315.77320.YahooMailNeo at web162405.mail.bf1.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi all,
>
> There is an unnatural sidechain in my input file, so I added new lines as
> new-defined(DPP) residue to the .rtp and .hdb files.
> Also there were some missed bonds, angles, and dihedrals in generated .top
> file, which manually added in.
> When I go through the grompp to do EM, I find a fatal error about the new
> defined residue:
>
> No default U-B types
>
> As I checked this kind of angle, it exists in other residues such as
> lysine as well. This angle is (defined by atom types):?
> CT1 CT2 NH3
>
>
> I checked the atom names, It seems ok.
>
> Part of the top file is as follow:
>
> ?residue?? 1 DPP rtp DPP? q +2.0
> ???? 1??????? NH3????? 1??? DPP????? N????? 1?????? -0.3???? 14.007?? ;
> qtot -0.3
> ???? 2???????? HC????? 1??? DPP???? H1????? 2?????? 0.33????? 1.008?? ;
> qtot 0.03
> ???? 3???????? HC????? 1??? DPP???? H2????? 3?????? 0.33????? 1.008?? ;
> qtot 0.36
> ???? 4???????? HC????? 1??? DPP???? H3????? 4?????? 0.33????? 1.008?? ;
> qtot 0.69
> ???? 5??????? CT1????? 1??? DPP???? CA????? 5?????? 0.21???? 12.011?? ;
> qtot 0.9
> ???? 6???????? HB????? 1??? DPP???? HA????? 6??????? 0.1????? 1.008?? ;
> qtot 1
> ???? 7??????? CT2????? 1??? DPP???? CB????? 7?????? 0.21???? 12.011?? ;
> qtot 1.21
> ???? 8???????? HA????? 1??? DPP??? HB1????? 8?????? 0.05????? 1.008?? ;
> qtot 1.26
> ???? 9???????? HA????? 1??? DPP??? HB2????? 9?????? 0.05????? 1.008?? ;
> qtot 1.31
> ??? 10??????? NH3????? 1??? DPP???? NG???? 10?????? -0.3???? 14.007?? ;
> qtot 1.01
> ??? 11???????? HC????? 1??? DPP??? HG1???? 11?????? 0.33????? 1.008?? ;
> qtot 1.34
> ??? 12???????? HC????? 1??? DPP??? HG2???? 12?????? 0.33????? 1.008?? ;
> qtot 1.67
> ??? 13???????? HC????? 1??? DPP??? HG3???? 13?????? 0.33????? 1.008?? ;
> qtot 2
> ??? 14????????? C????? 1??? DPP????? C???? 14?????? 0.51???? 12.011?? ;
> qtot 2.51
> ??? 15????????? O????? 1??? DPP????? O???? 15????? -0.51???? 15.999?? ;
> qtot 2
>
> Fatal error:
> ERROR 1 [file topol.top, line 853]:
> ? No default U-B types
>
> line 853: ??? 5???? 7??? 10???? 5
>
>
>
> Would you please let me your suggestions about the reason of this error?
> How can I pass it? Would you please help me?
>
> Thanks in advance for your suggestions.
>
> Sincerely,
> Shima?
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 22 Apr 2014 12:31:46 +0530
> From: Venkat Reddy <venkat4bt at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Fwd: Concatenating two trajectories
> Message-ID:
> <CAFhLg7WyUOnpo8SgS7kMkObxCytBuHrYO6RPiQUKRQvrGS0=
> 8A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> No, By default it will give the starting time from where it started. I
> doubt your simulation extension has some problem. The commands to extend a
> simulation are
> tpbconv -s old.tpr -extend <time in ps> -o new.tpr
> mdrun -v -s new.tpr -cpi state.cpt -deffnm new
>
> Hope it will help you.
>
>
> On Tue, Apr 22, 2014 at 11:00 AM, Sunita <sunita.bio at gmail.com> wrote:
>
> > Hello Venkat,
> >
> > Yeah, I think by default it will give 0 ps as start time for both
> > trajectories and it should be set by user using -settime flag
> > Correct me if I am wrong.
> >
> > Regards
> >
> > --
> > View this message in context:
> >
> http://gromacs.5086.x6.nabble.com/Fwd-Concatenating-two-trajectories-tp5015956p5015992.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 22 Apr 2014 10:25:19 +0200
> From: Rossen Apostolov <rossen at kth.se>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>,
> Discussion list for GROMACS development <
> gmx-developers at gromacs.org>
> Subject: [gmx-users] deprecating the Nabble forums
> Message-ID: <5356276F.8030104 at kth.se>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Hi everyone,
>
> A few years ago we integrated the gmx-users and gmx-developers mailing
> lists (handled by mailman) with the Nabble platform. The goal was to
> provide a convenient search interface and means for new users to
> participate in earlier discussions.
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> There's not much point in keeping the extra interface so we will
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> We plan to do that _next week_ so if you have used only the forums so
> far, please subscribe to the users lists at
>
> https://mailman-1.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
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>
> Cheers,
> Rossen
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 22 Apr 2014 09:50:39 +0100
> From: Erik Marklund <erik.marklund at chem.ox.ac.uk>
> To: <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] negative HB lifetime
> Message-ID: <B9948909-4E58-4097-BC52-FC260CE4E13B at chem.ox.ac.uk>
> Content-Type: text/plain; charset=us-ascii
>
> Hi,
>
> To clarify: Note that the ACF should approach zero for large t. It seems
> your ACF isn't approaching zero in the way that fits with Luzar and
> Chandler's model. The reason for that may be insufficient sampling of
> hydrogen bonds over time, in which case you need more data either by
> extending the simulations or using larger analysis groups if possible; or
> perhaps you save the coordinated too infrequently, which makes a bad ACF.
> Alternatively, the hb-kinetics in your system isn't well described by the
> kinetic model, in which case better sampling will not help you.
>
> Erik
>
> On 21 Apr 2014, at 15:51, Erik Marklund <erik.marklund at chem.ox.ac.uk>
> wrote:
>
> > Hi,
> >
> > Yes. Or use larger analysis groups if possible.
> >
> > Kind regards,
> > Erik
> >
> > On 17 Apr 2014, at 10:58, Djamila <benrezkallah at gmail.com> wrote:
> >
> >> Thanks Erik;
> >> You're alright, The problem is in the ACF; it falls dramatically to
> zero.
> >> In this case, what's the solution? should I extend my simulation to more
> >> time?
> >> Thanks
> >>
> >> Djamila
> >>
> >> --
> >> View this message in context:
> http://gromacs.5086.x6.nabble.com/negative-HB-lifetime-tp5015830p5015900.html
> >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >>
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> > --
> > Gromacs Users mailing list
> >
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>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 22 Apr 2014 05:52:56 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org, Shima Arasteh <shima_arasteh2001 at yahoo.com>
> Subject: Re: [gmx-users] No default U-B types
> Message-ID: <53563BF8.9090205 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 4/22/14, 2:31 AM, Shima Arasteh wrote:
> > Hi all,
> >
> > There is an unnatural sidechain in my input file, so I added new lines
> as new-defined(DPP) residue to the .rtp and .hdb files.
> > Also there were some missed bonds, angles, and dihedrals in generated
> .top file, which manually added in.
> > When I go through the grompp to do EM, I find a fatal error about the
> new defined residue:
> >
> > No default U-B types
> >
> > As I checked this kind of angle, it exists in other residues such as
> lysine as well. This angle is (defined by atom types):
> > CT1 CT2 NH3
> >
>
> That angle doesn't exist in other amino acids. For lysine, CT2-CT2-NH3
> exists,
> but not CT1-CT2-NH3. You'll have to add parameters for this angle, and
> probably
> a few dihedrals, as well.
>
> -Justin
>
> >
> > I checked the atom names, It seems ok.
> >
> > Part of the top file is as follow:
> >
> > residue 1 DPP rtp DPP q +2.0
> > 1 NH3 1 DPP N 1 -0.3 14.007 ;
> qtot -0.3
> > 2 HC 1 DPP H1 2 0.33 1.008 ;
> qtot 0.03
> > 3 HC 1 DPP H2 3 0.33 1.008 ;
> qtot 0.36
> > 4 HC 1 DPP H3 4 0.33 1.008 ;
> qtot 0.69
> > 5 CT1 1 DPP CA 5 0.21 12.011 ;
> qtot 0.9
> > 6 HB 1 DPP HA 6 0.1 1.008 ;
> qtot 1
> > 7 CT2 1 DPP CB 7 0.21 12.011 ;
> qtot 1.21
> > 8 HA 1 DPP HB1 8 0.05 1.008 ;
> qtot 1.26
> > 9 HA 1 DPP HB2 9 0.05 1.008 ;
> qtot 1.31
> > 10 NH3 1 DPP NG 10 -0.3 14.007 ;
> qtot 1.01
> > 11 HC 1 DPP HG1 11 0.33 1.008 ;
> qtot 1.34
> > 12 HC 1 DPP HG2 12 0.33 1.008 ;
> qtot 1.67
> > 13 HC 1 DPP HG3 13 0.33 1.008 ;
> qtot 2
> > 14 C 1 DPP C 14 0.51 12.011 ;
> qtot 2.51
> > 15 O 1 DPP O 15 -0.51 15.999 ;
> qtot 2
> >
> > Fatal error:
> > ERROR 1 [file topol.top, line 853]:
> > No default U-B types
> >
> > line 853: 5 7 10 5
> >
> >
> >
> > Would you please let me your suggestions about the reason of this error?
> How can I pass it? Would you please help me?
> >
> > Thanks in advance for your suggestions.
> >
> > Sincerely,
> > Shima
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> --
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> End of gromacs.org_gmx-users Digest, Vol 120, Issue 95
> ******************************************************
>
--
--
SUNITA GUPTA
Senior Research Fellow
Bioinformatics Centre
Jawaharlal Nehru University
New Delhi- 110067
Email- sunita.bio at gmail.com
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