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-requ...@gromacs.org> > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 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 <lida...@gmail.com> > Subject: Re: [gmx-users] scaling non-bonded interactions > To: jalem...@vt.edu, Discussion list for GROMACS users > <gmx-users@gromacs.org> > Message-ID: <BANLkTinww3_rE7x-SyffAPY=rwpyxt2...@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 <jalem...@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@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-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110601/3f9a1391/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Wed, 1 Jun 2011 15:34:49 -0400 > From: Miguel Quiliano Meza <rifaxim...@gmail.com> > Subject: [gmx-users] question about trajcat command: Merge files > To: gmx-users@gromacs.org > Message-ID: <BANLkTi=ai0nowvv_g3evvxxuqb1kcda...@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. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110601/6e593040/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Wed, 01 Jun 2011 15:35:34 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Re: scaling non-bonded interactions > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4de69486.5070...@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 <jalem...@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" <jalem...@vt.edu> > Subject: Re: [gmx-users] scaling non-bonded interactions > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4de69529.6000...@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 <jalem...@vt.edu > > <mailto:jalem...@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@gromacs.org > > <mailto:gmx-users@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-requ...@gromacs.org > > <mailto:gmx-users-requ...@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" <jalem...@vt.edu> > Subject: Re: [gmx-users] question about trajcat command: Merge files > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4de695bd.7030...@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.ku...@herts.ac.uk> > Subject: RE: [gmx-users] Re: scaling non-bonded interactions > To: "vvcha...@gmail.com" <vvcha...@gmail.com>, Discussion list for > GROMACS users <gmx-users@gromacs.org> > Message-ID: > <2f848dc922c8d741bf3a60b7d7108b6a9ef2ac3...@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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On > Behalf Of Vitaly Chaban [vvcha...@gmail.com] > Sent: 01 June 2011 20:30 > To: jalem...@vt.edu > Cc: gmx-users@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 <jalem...@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@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@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! > > End of gmx-users Digest, Vol 86, Issue 10 > ***************************************** >
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