[gmx-users] Re: question about trajcat command: Merge files
Miguel Quiliano Meza
rifaximina at gmail.com
Wed Jun 1 23:27:18 CEST 2011
Dear Justin.
Thank you for you answer.
But, the case I wrote, it was an ideally case. To help anyone in the forum
at the same time.
As soon as I have read your answer I tried. In my case my simulations were:
First simulation: 0.4ns
Second : 1ns
Third: 2ns
Fourth: 10ns
----------------------
Total = 13.4ns
So I planned to do an RMSD plot of 0-13.4ns. As I said before, each
simulation is the continuation of the previous, obviously to do this I used
checkpoint files for each simulation and the same MD.mdp, only changed the
time of simulation.
I did:
trajcat -f md_0_4ns_noPBC.xtc md_1ns_noPBC.xtc md_2ns_noPBC.xtc
md_10ns_noPBC.xtc -o TOTAL_13_4ns_noPBC.xtc
Then for curiosity I did > ls -lh
rw-r--r-- 1 willy bioinfo 368M 2011-06-01 13:10 md_0_4_noPBC.xtc
-rw-r--r-- 1 willy bioinfo 917M 2011-06-01 13:12 md_1ns_noPBC.xtc
-rw-r--r-- 1 willy bioinfo 917M 2011-06-01 13:13 md_2ns_noPBC.xtc
-rw-r--r-- 1 willy bioinfo 9.0G 2011-06-01 13:17 md_10ns_noPDB.xtc
-rw-r--r-- 1 willy bioinfo 9.0G 2011-06-01 15:44 TOTAL_13_4ns_noPBC.xtc
Surprisingly the file "TOTAL_13_4ns_noPBC.xtc" had the same size of the file
"md_10ns_noPDB.xtc", is it normal?
Continue with the process, then:
>g_rms -s molecule_sol_ion_MD_0_4ns.tpr -f TOTAL_13_4ns_noPDB.xtc -o
rmsd_13_4ns_molecule.xvg -tu ns
I open the .XVG as a simple .txt and I noticed that the time only reach 10ns
or 10000ps. Why not 13.4ns?
I would be very grateful If you can tell me what is happening.
Thanks in adavance.
Miguel Quiliano.
2011/6/1 <gmx-users-request at gromacs.org>
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> Today's Topics:
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> 1. Re: scaling non-bonded interactions (Da-Wei Li)
> 2. question about trajcat command: Merge files (Miguel Quiliano Meza)
> 3. Re: Re: scaling non-bonded interactions (Justin A. Lemkul)
> 4. Re: scaling non-bonded interactions (Justin A. Lemkul)
> 5. Re: question about trajcat command: Merge files (Justin A. Lemkul)
> 6. RE: Re: scaling non-bonded interactions (Kukol, Andreas)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 1 Jun 2011 15:32:07 -0400
> From: Da-Wei Li <lidawei at gmail.com>
> Subject: Re: [gmx-users] scaling non-bonded interactions
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <BANLkTinww3_rE7x-SyffAPY=RWPyxt2-5A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> I remember that 1-4 won't be scaled in the free energy code, right?
>
> dawei
>
> On Wed, Jun 1, 2011 at 3:24 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > Kukol, Andreas wrote:
> >
> >> Hello,
> >> Is it possible to globally scale all non-bonded interactions by a factor
> ?
> >> I know there are energy exclusion groups, but that is an all or nothing
> >> approach, while I would like to reduce non-bonded interaction potentials
> to
> >> e.g. 10% of their normal value.
> >>
> >> If this is not possible, I suggest to have this as an option in the
> >> mdp-file.
> >>
> >>
> > You can do this with the free energy code.
> >
> > couple-moltype = system
> > init_lambda = 0.9
> > couple_lambda0 = vdw-q
> > couple_lambda1 = none
> >
> > Please note, though, that such settings will result in massive
> performance
> > loss, even for small systems. There is an open issue on the redmine
> server
> > about this, but no resolution yet.
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > 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 at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
> >
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> ------------------------------
>
> Message: 2
> Date: Wed, 1 Jun 2011 15:34:49 -0400
> From: Miguel Quiliano Meza <rifaximina at gmail.com>
> Subject: [gmx-users] question about trajcat command: Merge files
> To: gmx-users at gromacs.org
> Message-ID: <BANLkTi=ai0noWVV_g3Evvxxuqb1kCdAmTA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear community,
>
> I have a couple of doubts, please help me to clarify.
>
> I performed 4 MD simulations using Gromacs (each one of 1ns, 2ns, 3ns ,4ns)
> , they are only a continuation of the last, because of I was explored the
> rmsd variation along the time. Now I want to merge all the trajectories to
> do only one plot of 10ns.
>
> So, I did:
>
> trajcat -f md_1ns_noPBC.xtc md_2ns_noPBC.xtc md_3ns_noPBC.xtc
> md_4ns_noPBC.xtc -o TOTAL_10ns_noPBC.xtc
>
> The program showed this:
>
> File Start time Time step
> ---------------------------------------------------------
> md_1ns_noPBC.xtc 0.000 ps 2.000 ps
> md_2ns_noPBC.xtc 0.000 ps 2.000 ps WARNING: same
> Start time as previous
> md_3ns_noPBC.xtc 0.000 ps 2.000 ps WARNING: same
> Start time as previous
> md_4ns_noPDB.xtc 0.000 ps 2.000 ps WARNING: same
> Start time as previous
>
> I am worry about the message 'WARNING: same Start time as previous', I
> think
> is normal because each simulation is like independent, that is the reason
> why start time is take as 0ps.
>
> Please tell me If my command line is correct according to my purposes. By
> the way, to make the plot (RMSD 10ns) I plan to do it with -s md_1ns.tpr,
> is
> it correct?
>
> Thank you in advance.
>
> Miguel Quiliano.
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> ------------------------------
>
> Message: 3
> Date: Wed, 01 Jun 2011 15:35:34 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: scaling non-bonded interactions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DE69486.5070203 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Vitaly Chaban wrote:
> > Doesn't increased temperature work for this purpose?
> >
> >
>
> REMD can be useful, yes, but generalized Hamiltonian exchange, using lambda
> to
> scale the interactions between molecules can be very effective, as well.
>
> -Justin
>
> >
> > On Wed, Jun 1, 2011 at 3:27 PM, Justin A. Lemkul <jalemkul at vt.edu>
> wrote:
> >>
> >> Vitaly Chaban wrote:
> >>>> Is it possible to globally scale all non-bonded interactions by a
> factor
> >>>> ? I know there are energy exclusion groups, but that is an all or
> nothing
> >>>> approach, while I would like to reduce non-bonded interaction
> potentials to
> >>>> e.g. 10% of their normal value.
> >>>>
> >>>> If this is not possible, I suggest to have this as an option in the
> >>>> mdp-file.
> >>>
> >>> I don't see much sense in such uniform scaling.
> >>>
> >>>
> >> Such scaling can be useful for overcoming energy barriers and speeding
> up
> >> equilibration. This function is hinted at in the description of the
> >> couple-moltype .mdp keyword. I don't know if that's the intent here,
> but it
> >> certainly does have an application.
> >>
> >> -Justin
> >>
> >> --
> >> ========================================
> >>
> >> Justin A. Lemkul
> >> Ph.D. Candidate
> >> ICTAS Doctoral Scholar
> >> MILES-IGERT Trainee
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >> ========================================
> >>
> >
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 01 Jun 2011 15:38:17 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] scaling non-bonded interactions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DE69529.6000801 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> Da-Wei Li wrote:
> > I remember that 1-4 won't be scaled in the free energy code, right?
> >
>
> True, but the desired 10% scaling in this case can be applied by changing
> the
> FudgeLJ and FudgeQQ values of the force field, I believe.
>
> -Justin
>
> > dawei
> >
> > On Wed, Jun 1, 2011 at 3:24 PM, Justin A. Lemkul <jalemkul at vt.edu
> > <mailto:jalemkul at vt.edu>> wrote:
> >
> >
> >
> > Kukol, Andreas wrote:
> >
> > Hello,
> > Is it possible to globally scale all non-bonded interactions by
> > a factor ? I know there are energy exclusion groups, but that
> > is an all or nothing approach, while I would like to reduce
> > non-bonded interaction potentials to e.g. 10% of their normal
> value.
> >
> > If this is not possible, I suggest to have this as an option in
> > the mdp-file.
> >
> >
> > You can do this with the free energy code.
> >
> > couple-moltype = system
> > init_lambda = 0.9
> > couple_lambda0 = vdw-q
> > couple_lambda1 = none
> >
> > Please note, though, that such settings will result in massive
> > performance loss, even for small systems. There is an open issue on
> > the redmine server about this, but no resolution yet.
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> > <tel:%28540%29%20231-9080>
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/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
> > <mailto:gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 01 Jun 2011 15:40:45 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] question about trajcat command: Merge files
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DE695BD.7030304 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Miguel Quiliano Meza wrote:
> > Dear community,
> >
> > I have a couple of doubts, please help me to clarify.
> >
> > I performed 4 MD simulations using Gromacs (each one of 1ns, 2ns, 3ns
> > ,4ns) , they are only a continuation of the last, because of I was
> > explored the rmsd variation along the time. Now I want to merge all the
> > trajectories to do only one plot of 10ns.
> >
> > So, I did:
> >
> > trajcat -f md_1ns_noPBC.xtc md_2ns_noPBC.xtc md_3ns_noPBC.xtc
> > md_4ns_noPBC.xtc -o TOTAL_10ns_noPBC.xtc
> >
> > The program showed this:
> >
> > File Start time Time step
> > ---------------------------------------------------------
> > md_1ns_noPBC.xtc 0.000 ps 2.000 ps
> > md_2ns_noPBC.xtc 0.000 ps 2.000 ps WARNING: same
> > Start time as previous
> > md_3ns_noPBC.xtc 0.000 ps 2.000 ps WARNING: same
> > Start time as previous
> > md_4ns_noPDB.xtc 0.000 ps 2.000 ps WARNING: same
> > Start time as previous
> >
> > I am worry about the message 'WARNING: same Start time as previous', I
> > think is normal because each simulation is like independent, that is the
> > reason why start time is take as 0ps.
> >
>
> This may be correct for your case (if in the .mdp file you have "tinit =
> 0") or
> you otherwise did not properly continue the simulation using a checkpoint
> file.
> If it makes sense to concatenate independent trajectories and consider
> them to
> be continuous, you can override the start times with the -settime option.
>
> > Please tell me If my command line is correct according to my purposes.
> > By the way, to make the plot (RMSD 10ns) I plan to do it with -s
> > md_1ns.tpr, is it correct?
> >
>
> That will calculate RMSD relative to the structure contained in the .tpr
> file
> that began the first 1-ns simulation. If that's what you wish to measure,
> then
> you're correct.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 1 Jun 2011 20:34:46 +0100
> From: "Kukol, Andreas" <a.kukol at herts.ac.uk>
> Subject: RE: [gmx-users] Re: scaling non-bonded interactions
> To: "vvchaban at gmail.com" <vvchaban at gmail.com>, Discussion list for
> GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <2F848DC922C8D741BF3A60B7D7108B6A9EF2AC3578 at UH-MAILSTOR.herts.ac.uk
> >
> Content-Type: text/plain; charset="us-ascii"
>
> I want to use it to energy minimise a system that has severe clashes. The
> EM always crashes, even if I reduce the step-size. It could also be useful
> for NMR refinement to allow atoms to move through each other in order to
> satisfy distance restraints.
>
> Andreas
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On
> Behalf Of Vitaly Chaban [vvchaban at gmail.com]
> Sent: 01 June 2011 20:30
> To: jalemkul at vt.edu
> Cc: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Re: scaling non-bonded interactions
>
> Doesn't increased temperature work for this purpose?
>
>
>
> On Wed, Jun 1, 2011 at 3:27 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> > Vitaly Chaban wrote:
> >>>
> >>> Is it possible to globally scale all non-bonded interactions by a
> factor
> >>> ? I know there are energy exclusion groups, but that is an all or
> nothing
> >>> approach, while I would like to reduce non-bonded interaction
> potentials to
> >>> e.g. 10% of their normal value.
> >>>
> >>> If this is not possible, I suggest to have this as an option in the
> >>> mdp-file.
> >>
> >>
> >> I don't see much sense in such uniform scaling.
> >>
> >>
> >
> > Such scaling can be useful for overcoming energy barriers and speeding up
> > equilibration. This function is hinted at in the description of the
> > couple-moltype .mdp keyword. I don't know if that's the intent here, but
> it
> > certainly does have an application.
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> >
>
>
>
> --
> Dr. Vitaly V. Chaban, Department of Chemistry
> University of Rochester, Rochester, New York 14627-0216
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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> 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/Support/Mailing_Lists
>
>
> ------------------------------
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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