[gmx-users] gromacs.org_gmx-users Digest, Vol 137, Issue 14
tasneem kausar
tasneemkausar12 at gmail.com
Thu Sep 3 06:21:12 CEST 2015
I want to see the change in secondary structure of the protein in vacuum as
well as in specific solvent.
On Wed, Sep 2, 2015 at 4:05 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. vacuum simulations (tasneem kausar)
> 2. demux.pl input file (Nawel Mele)
> 3. Re: trjconv -pbc nojump (Ganesh Shahane)
> 4. Re: demux.pl input file (Andrea P?rez-Villa)
> 5. Re: vacuum simulations (Jo?o Henriques)
> 6. Re: demux.pl input file (Nawel Mele)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 2 Sep 2015 15:36:52 +0530
> From: tasneem kausar <tasneemkausar12 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] vacuum simulations
> Message-ID:
> <
> CAFaK4UbfKk5M3B1bCWRNgwg6_p3xgw5dzAvR75LiU1HL66+MLg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear gromacs users
>
> I have performed the vacuum simulation of protein.
> The structure was minimized after generating the box using the following
> mdp parameters.
> ;
> ; User spoel (236)
> ; Wed Nov 3 17:12:44 1993
> ; Input file
> ;
> cpp = /usr/bin/cpp
> define = -DFLEX_SPC
> constraints = hbonds
> integrator = steep
> nsteps = 3000
> ;
> ; Energy minimizing stuff
> ;
> emtol = 2000
> emstep = 0.01
>
> nstcomm = 1
> ns_type = simple
> rlist = 0.0
> coulombtype = cut-off
> rcoulomb = 0.0
> rvdw = 0.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> Tcoupl = no
> Pcoupl = no
> PBC = no
> gen_vel = no
>
>
> then i have run the full md for 5ns.
> mdp parameter are as follows:
>
> ;
> ; User spoel (236)
> ; Wed Nov 3 17:12:44 1993
> ; Input file
> ;
> title = Yo
> cpp = /usr/bin/cpp
> constraints = hbonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 2500000 ; total 5000 ps.
> nstcomm = 1
> nstxout = 500000
> nstvout = 500000
> comm-mode = ANGULAR
> lincs_iter = 2
> nstfout = 0
> nstlog = 500
> nstenergy = 500
> nstxtcout = 500
> xtc-precision = 1000
> nstlist = 10
> ns_type = simple
> rlist = 0.0
> coulombtype = cut-off
> rcoulomb = 0.0
> rvdw = 0.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = no
> tc-grps = Protein
> tau_t = 0.1
> ref_t = 300
> ; Energy monitoring
> energygrps = Protein
> ; Isotropic pressure coupling is now on
> Pcoupl = no
> Pcoupltype = isotropic
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is off at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
> PBC = no
>
>
> Is this a right way to perform the MD in vacuum?
> Anyone if familiar with this procedure, please suggest.
>
>
> Thanks in Advance
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 2 Sep 2015 11:16:11 +0100
> From: Nawel Mele <nawel.mele at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: [gmx-users] demux.pl input file
> Message-ID:
> <
> CAJTRp+o9qJ0+6sjs73_doE9xUAnRVcxMGeo1QKOCTyM2L5GZrw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Users,
>
> I have performed a REMD simulation on a protein with 48 replicas. I have
> 400ns of REMD simulation and by consequence several restart simulation and
> so several .log files:
>
> run1_0.log , run1_0.log .... run1_47.log
> run2_0.log , run2_0.log .... run2_47.log
> .
> .
> .
> runx_0.log , runx_0.log .... runx_47.log
>
> I am interested on the lowest temperature trajectory and I want to use the
> demux.pl scriot.
> I have been through many similar questions in the forum but I am still
> confused how to use the demux.pl script.
> Should I need to concatenate all my log files like this:
>
> cat run1_1.log run2_1.log ... runx_1.log > run_total.log
>
> cat run1_0.log run1_1.log run1_2.log ... run1_47.log
> run2_0.log run2_1.log run2_2.log ... run2_47.log ...
> runx_0.log runx_1.log runx_2.log ...runx_47.log > run_total.log
>
> Many thanks for your help.
>
> Nawel
>
>
>
>
>
> --
>
> Nawel Mele, PhD Research Student
>
> Jonathan Essex Group, School of Chemistry
>
> University of Southampton, Highfield
>
> Southampton, SO17 1BJ
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 2 Sep 2015 15:49:11 +0530
> From: Ganesh Shahane <ganesh7shahane at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] trjconv -pbc nojump
> Message-ID:
> <CAEW0SHbadaV2weKy8smc2JaR3=
> 4otWAiVD0E6bh60hk7gBwgRQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Reisser,
>
> Instead of using -pbc nojump, use -pbc whole.
>
> On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) <
> sabine.reisser at kit.edu> wrote:
>
> > Hi,
> >
> >
> > I want to use trjconv -pbc nojump to create a trajectory without box
> > jumping of molecules. The molecules (lipids) also start to diffuse out of
> > the box like they should, but in some a part of the molecule still jumps
> > (as I could observe in xy direction), while the rest doesn't, leading to
> > artificially long bonds in VMD. I tried trjconv -pbc nojump both with a
> tpr
> > file in the -s option, or a gro file (with only complete molecules), same
> > result.
> >
> >
> > I'd be glad if somebody could give me a hint.
> >
> >
> > Cheers
> >
> > Sabine
> >
> >
> >
> > --
> > Dr. Sabine Rei?er
> > Theoretical Chemical Biology
> > Institute of Physical Chemistry
> > Karlsruhe Institute of Technology
> >
> > --
> > 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 gmx-users-request at gromacs.org.
> >
>
>
>
> --
> Best Regards,
> Ganesh Shahane
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 2 Sep 2015 12:26:26 +0200
> From: Andrea P?rez-Villa <a.pervilla at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] demux.pl input file
> Message-ID:
> <CAJ2wbWa5qM+-jU14tMuK76Ms-uV4vPjkZST=bTPD=
> QOZfdbT+A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Nawel,
> You need to concatenate the log files of replica "0".
> Regards,
>
> Andrea
>
> 2015-09-02 12:16 GMT+02:00 Nawel Mele <nawel.mele at gmail.com>:
>
> > Dear Users,
> >
> > I have performed a REMD simulation on a protein with 48 replicas. I have
> > 400ns of REMD simulation and by consequence several restart simulation
> and
> > so several .log files:
> >
> > run1_0.log , run1_0.log .... run1_47.log
> > run2_0.log , run2_0.log .... run2_47.log
> > .
> > .
> > .
> > runx_0.log , runx_0.log .... runx_47.log
> >
> > I am interested on the lowest temperature trajectory and I want to use
> the
> > demux.pl scriot.
> > I have been through many similar questions in the forum but I am still
> > confused how to use the demux.pl script.
> > Should I need to concatenate all my log files like this:
> >
> > cat run1_1.log run2_1.log ... runx_1.log > run_total.log
> >
> > cat run1_0.log run1_1.log run1_2.log ... run1_47.log
> > run2_0.log run2_1.log run2_2.log ... run2_47.log ...
> > runx_0.log runx_1.log runx_2.log ...runx_47.log > run_total.log
> >
> > Many thanks for your help.
> >
> > Nawel
> >
> >
> >
> >
> >
> > --
> >
> > Nawel Mele, PhD Research Student
> >
> > Jonathan Essex Group, School of Chemistry
> >
> > University of Southampton, Highfield
> >
> > Southampton, SO17 1BJ
> > --
> > 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 gmx-users-request at gromacs.org.
> >
>
>
>
> --
> Andrea P?rez Villa
> *"Res non Verba"*
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 2 Sep 2015 12:28:24 +0200
> From: Jo?o Henriques <joao.henriques.32353 at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] vacuum simulations
> Message-ID:
> <
> CALC+HGSeF+7aSJZPbsnU+c6QHXB+4SAAszh4pMgwu_RR1qc-Cw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Tasneem,
>
> Like on previous replies to your last email, people need to understand what
> is the purpose of your simulation(s), otherwise it is difficult to help.
> "Cooking" and "simulating" are two completely different things, there is no
> recipe for the latter. One needs to understand what one wants to do in the
> first place, and then what each parameter means and how it influences the
> results. One should never fall into the temptation of using someone else's
> .mdp files blindly. Many things have become *de facto* over the years, most
> of the times for no other good reason besides the fact that some important
> name in the field has been using it...
>
> Best regards,
> Jo?o
>
> On Wed, Sep 2, 2015 at 12:06 PM, tasneem kausar <tasneemkausar12 at gmail.com
> >
> wrote:
>
> > Dear gromacs users
> >
> > I have performed the vacuum simulation of protein.
> > The structure was minimized after generating the box using the following
> > mdp parameters.
> > ;
> > ; User spoel (236)
> > ; Wed Nov 3 17:12:44 1993
> > ; Input file
> > ;
> > cpp = /usr/bin/cpp
> > define = -DFLEX_SPC
> > constraints = hbonds
> > integrator = steep
> > nsteps = 3000
> > ;
> > ; Energy minimizing stuff
> > ;
> > emtol = 2000
> > emstep = 0.01
> >
> > nstcomm = 1
> > ns_type = simple
> > rlist = 0.0
> > coulombtype = cut-off
> > rcoulomb = 0.0
> > rvdw = 0.0
> > fourierspacing = 0.12
> > fourier_nx = 0
> > fourier_ny = 0
> > fourier_nz = 0
> > pme_order = 4
> > ewald_rtol = 1e-5
> > optimize_fft = yes
> > Tcoupl = no
> > Pcoupl = no
> > PBC = no
> > gen_vel = no
> >
> >
> > then i have run the full md for 5ns.
> > mdp parameter are as follows:
> >
> > ;
> > ; User spoel (236)
> > ; Wed Nov 3 17:12:44 1993
> > ; Input file
> > ;
> > title = Yo
> > cpp = /usr/bin/cpp
> > constraints = hbonds
> > integrator = md
> > dt = 0.002 ; ps !
> > nsteps = 2500000 ; total 5000 ps.
> > nstcomm = 1
> > nstxout = 500000
> > nstvout = 500000
> > comm-mode = ANGULAR
> > lincs_iter = 2
> > nstfout = 0
> > nstlog = 500
> > nstenergy = 500
> > nstxtcout = 500
> > xtc-precision = 1000
> > nstlist = 10
> > ns_type = simple
> > rlist = 0.0
> > coulombtype = cut-off
> > rcoulomb = 0.0
> > rvdw = 0.0
> > fourierspacing = 0.12
> > fourier_nx = 0
> > fourier_ny = 0
> > fourier_nz = 0
> > pme_order = 4
> > ewald_rtol = 1e-5
> > optimize_fft = yes
> > ; Berendsen temperature coupling is on in two groups
> > Tcoupl = no
> > tc-grps = Protein
> > tau_t = 0.1
> > ref_t = 300
> > ; Energy monitoring
> > energygrps = Protein
> > ; Isotropic pressure coupling is now on
> > Pcoupl = no
> > Pcoupltype = isotropic
> > tau_p = 0.5
> > compressibility = 4.5e-5
> > ref_p = 1.0
> > ; Generate velocites is off at 300 K.
> > gen_vel = yes
> > gen_temp = 300.0
> > gen_seed = 173529
> > PBC = no
> >
> >
> > Is this a right way to perform the MD in vacuum?
> > Anyone if familiar with this procedure, please suggest.
> >
> >
> > Thanks in Advance
> > --
> > 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 gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 2 Sep 2015 11:35:21 +0100
> From: Nawel Mele <nawel.mele at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] demux.pl input file
> Message-ID:
> <
> CAJTRp+psQ0dw+Oyd2PA4tGcJhwqC+nr2Ox9seO1257nnVPgvYQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Andrea,
>
> Thank you very much for your quick answer.
>
> I would like to ask you another quick question. Like I said I am interested
> on a particular temperature , so I wanted to use the demux.pl file to
> follow the trajectory of my temperature of interest through the temperature
> space.
> But, if I want the trajectory of this specific temperature in order to
> perform different analysis on it like dihedral and hydrogen bond analysis.
> Should I use first demux.pl on the replica "0" (for the lowest
> temperature)
> and then use the replica_index.xvg output file and perform : trjcat -f
> *.trr -demux replica_index.xvg or because during gromacs REMD simulation
> only coordinates are exchanges do I need to use the demux.pl script for
> extracting my trajectory??
>
> Thanks again,
>
> Nawel
>
>
> 2015-09-02 11:26 GMT+01:00 Andrea P?rez-Villa <a.pervilla at gmail.com>:
>
> > Dear Nawel,
> > You need to concatenate the log files of replica "0".
> > Regards,
> >
> > Andrea
> >
> > 2015-09-02 12:16 GMT+02:00 Nawel Mele <nawel.mele at gmail.com>:
> >
> > > Dear Users,
> > >
> > > I have performed a REMD simulation on a protein with 48 replicas. I
> have
> > > 400ns of REMD simulation and by consequence several restart simulation
> > and
> > > so several .log files:
> > >
> > > run1_0.log , run1_0.log .... run1_47.log
> > > run2_0.log , run2_0.log .... run2_47.log
> > > .
> > > .
> > > .
> > > runx_0.log , runx_0.log .... runx_47.log
> > >
> > > I am interested on the lowest temperature trajectory and I want to use
> > the
> > > demux.pl scriot.
> > > I have been through many similar questions in the forum but I am still
> > > confused how to use the demux.pl script.
> > > Should I need to concatenate all my log files like this:
> > >
> > > cat run1_1.log run2_1.log ... runx_1.log > run_total.log
> > >
> > > cat run1_0.log run1_1.log run1_2.log ... run1_47.log
> > > run2_0.log run2_1.log run2_2.log ... run2_47.log ...
> > > runx_0.log runx_1.log runx_2.log ...runx_47.log > run_total.log
> > >
> > > Many thanks for your help.
> > >
> > > Nawel
> > >
> > >
> > >
> > >
> > >
> > > --
> > >
> > > Nawel Mele, PhD Research Student
> > >
> > > Jonathan Essex Group, School of Chemistry
> > >
> > > University of Southampton, Highfield
> > >
> > > Southampton, SO17 1BJ
> > > --
> > > 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 gmx-users-request at gromacs.org.
> > >
> >
> >
> >
> > --
> > Andrea P?rez Villa
> > *"Res non Verba"*
> > --
> > 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 gmx-users-request at gromacs.org.
>
>
>
>
> --
>
> Nawel Mele, PhD Research Student
>
> Jonathan Essex Group, School of Chemistry
>
> University of Southampton, Highfield
>
> Southampton, SO17 1BJ
>
>
> ------------------------------
>
> --
> 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 gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 137, Issue 14
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