Re: [gmx-users] restart md from the point it had stopped
sarbani chattopadhyay wrote: hi, I have been running a molecular dynamics simulation for 2 nanoseconds.But it stopped in the middle because of an internal problem.Is there any way to restart the simulation from the point it has stopped? See http://wiki.gromacs.org/index.php/Doing_Restarts for an expanded discussion. Mark ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restart md from the point it had stopped
Hi Diego, gmxcheck will tell you whether the last frame is corrupted (incomplete) or not. Besides, why do you write velocities and forces every 10 ps? Do you have to much space on your hard-disk or do you need the velocities? Usually, writing to the .trr will be a compromise between the amount of disk space you have and the time you'll loose when restarting. I usually write one or two frames to the .trr per day. Cheers, Tsjerk On 10/8/07, Diego Enry <[EMAIL PROTECTED]> wrote: > > gmxcheck -f broken.trr > > check this information: > > Item#frames Timestep (ps) > Step 10110 > Time 10110 > Lambda10110 > Coords 10110 > Velocities 101 10 > Forces 101 10 > Box10110 > > I writing it every 1ps. > I recommend you NOT to use the LAST frame because it may be corrupted > if your simulation was terminated while writing this frame. To > continue, specify the frame just before the last one find above. > > tpbconv -s broken.tpr -f broken.trr -e broken.edr -o continue.tpr -time 9 > > Check If you write velocities&force to the .trr file, I think you > can't get a good continuation without that information. > > > On 10/8/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > > Hi Sarbani, > > > > Use tpbconv. You can only (properly) restart from a point where you have > a > > frame with velocities (in the .trr file) and preferrably energies > (.edr). > > > > Best, > > > > Tsjerk > > > > > > On 8 Oct 2007 12:34:23 -, sarbani chattopadhyay > > <[EMAIL PROTECTED]> wrote: > > > > > > > > > > > > > > > hi, > > > I have been running a molecular dynamics simulation for 2 > > nanoseconds.But it stopped in > > > the middle because of an internal problem.Is there any way to restart > the > > simulation from > > > the point it has stopped? > > > > >Thank all > > > > > Sarbani > > > > > > > > > ___ > > > gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > Junior UD (post-doc) > > Biomolecular NMR, Bijvoet Center > > Utrecht University > > Padualaan 8 > > 3584 CH Utrecht > > The Netherlands > > P: +31-30-2539931 > > F: +31-30-2537623 > > ___ > > gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > -- > Diego Enry B. Gomes > Laboratório de Modelagem e Dinamica Molecular > Universidade Federal do Rio de Janeiro - Brasil. > ___ > gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fwd: project 4
-- Forwarded message -- From: Wasef Muzaffar <[EMAIL PROTECTED]> Date: Oct 8, 2007 1:03 AM Subject: Fwd: project 4 To: Russell Green <[EMAIL PROTECTED]> -- Forwarded message -- From: Wasef Muzaffar <[EMAIL PROTECTED]> Date: Oct 17, 2006 10:22 PM Subject: Re: project 4 To: Jack Rogers <[EMAIL PROTECTED]> Cc: Me <[EMAIL PROTECTED]> I think I might not have send the updated one I was working with that included a print statement for the final cell. On 10/17/06, Wasef Muzaffar < [EMAIL PROTECTED]> wrote: > > Dear Dr. Rogers, > > I have attached the source code for project 4. > > GLHFormula9(2).cpp Description: Binary data ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox using tip5p water results in too few number of water molecules
JW Feng wrote: David, The results from using version 3.3.1 is different from version 3.3.2. In version 3.3.1, adding "SOL OL 0" and executing "genbox -cs tip5p.gro -box 1 1 1" created a box with 37 SOL molecules but the density is too high at 3072.87 g/L. In version 3.3.2, adding "SOL OL 0" did not work. However, I added "SOL LP0" to the end of vdwradii.dat and the resulting water box contained 37 SOL molecules. The density is incorrect at 2582.79 g/l. This box contains six more SOL molecules compared to a box created with TIP4P water. that is a coincidence. try with a larger box. the number is correct. JW On 10/7/07, David van der Spoel <[EMAIL PROTECTED]> wrote: JW Feng wrote: Hello, I used genbox (version 3.3.1 and 3.3.2) to create a 1nm box of SPC, TIP4P and TIP5P water with " genbox -cs .gro -box 1 1 1". The TIP5P box contains half the number of water molecules compared to TIP4P and SPC. SPC: 33 SOL molecules, density=987.205 (g/l) TIP4P: 31 SOL molecules TIP5P: 15 SOL molecules Can anyone please explain this? How do I get genbox to create a box with the right number of TIP5P water molecules. Thanks, JW It is because of the name of the lone pairs (OL) which is interpreted as an oxygen atom. You can add OL in vdwradii.dat with radius 0 and try again. Please report whether it works, then I will fix it in further releases. -- 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. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory
Hi Tanping, I don't know if that is the problem, but it could be. I think there was (and still may be) a reproducibility issue when using PME in GROMACS version 3.3.1 combined with FFTW3. See for instance the maillist posts (and subsequent threads) http://www.gromacs.org/pipermail/gmx-developers/2006-December/001986.htm l, http://www.gromacs.org/pipermail/gmx-developers/2007-January/001989.html and http://www.gromacs.org/pipermail/gmx-users/2007-May/027397.html. Some time ago I had the same problem with version 3.3.1 as you described (simulation results changing when only changing output parameters). But at that time I figured it was probably due to the abovementioned PME-issue, and didn't give it much attention. However, I'm definitely not the expert here, so I may be sending you in a totally wrong direction. Especially since you're using the much older 3.2.1 version, of which I don't know whether it has the same issue. So I guess my best advice to you at this moment would be to switch to the newest version (3.3.2) first and check whether the problem persists. Greetings, Jeroen >Date: Mon, 8 Oct 2007 06:07:28 -0700 (PDT) >From: Tanping Li <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Different nstxout and nstvout in mdp file > gives totally different trajectory >To: Discussion list for GROMACS users >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=iso-8859-1 > >Dear Jeroen, > >I am using gromacs-3.2.1, and PME. Is that the problem? > > >Yours >Tanping > > >--- van Bemmelen ><[EMAIL PROTECTED]> wrote: > >> Hi Tanping, >> >> This may seem irrelevant, but are you using PME? And which >version of >> GROMACS is it? >> >> Greetings, >> Jeroen >> >> >> >Date: Sun, 7 Oct 2007 08:46:04 -0700 (PDT) >> >From: Tanping Li <[EMAIL PROTECTED]> >> >Subject: Re: [gmx-users] Different nstxout and >> nstvout in mdp file >> >gives totally different trajectory >> >To: Discussion list for GROMACS users >> >> >Message-ID: >> <[EMAIL PROTECTED]> >> >Content-Type: text/plain; charset=iso-8859-1 >> > >> >Dear Tsjerk, >> > >> >Thanks for your help. >> > >> >I run the two jobs on a cluster, maybe on different >> nodes; >> > >> >After just a few hundreds ps, the coordinates of >> the system >> >differs a lot. When I calculate the distance >> between two >> >atoms, there is about 1.5A difference; >> > >> >Everything else in mdp file is exactly same. >> > >> > >> >Yours >> >Tanping ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] running gromacs in parallel, and with nice levels
On 10/4/2007 11:50 PM, maria goranovic wrote: Dear All, - So I "think" I succeeded in running gromacs on a 4-core node. How does one confirm this without looking at the speed. i.e, where is it mentioned in the log file what the number of processors is ? I do get 4 different log files for 4 processors, is that the final evidence ? Make sure that mdrun is compiled with mpi; other, it will result in four independent process, with four "different" log files (of course, in such case, log files could more or less the same.). - The nice level by default is too high (19). One can change this by compiling mdrun with a nonice option. However, does it really matter if one is running gromacs on a dedicated supercomputing node ? Also, one can change the nice level by -nice in the mdrun command. So, in principle, there is no need to recompile mdrun ? You don't need to re-compile mdrun in order to get rid of the "nice" effect. Setting nice to 19 for mdrun is alright, but I got a bit inefficiency with analysis tools at nice 19. This results in slow execution of the analysis tools when there is background jobs, e.g. mdrun. Thank you so very much for the inputs, -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restart md from the point it had stopped
gmxcheck -f broken.trr check this information: Item#frames Timestep (ps) Step 10110 Time 10110 Lambda10110 Coords 10110 Velocities 101 10 Forces 101 10 Box10110 I writing it every 1ps. I recommend you NOT to use the LAST frame because it may be corrupted if your simulation was terminated while writing this frame. To continue, specify the frame just before the last one find above. tpbconv -s broken.tpr -f broken.trr -e broken.edr -o continue.tpr -time 9 Check If you write velocities&force to the .trr file, I think you can't get a good continuation without that information. On 10/8/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Sarbani, > > Use tpbconv. You can only (properly) restart from a point where you have a > frame with velocities (in the .trr file) and preferrably energies (.edr). > > Best, > > Tsjerk > > > On 8 Oct 2007 12:34:23 -, sarbani chattopadhyay > <[EMAIL PROTECTED]> wrote: > > > > > > > > > > hi, > > I have been running a molecular dynamics simulation for 2 > nanoseconds.But it stopped in > > the middle because of an internal problem.Is there any way to restart the > simulation from > > the point it has stopped? > > >Thank all > > > Sarbani > > > > > > ___ > > gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > ___ > gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restart md from the point it had stopped
Please check the FAQ & list achives b4 posting. Your answer is already there. Is there any smart way to continue a run that crashed? http://www.gromacs.org/content/view/62/29/ -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restart md from the point it had stopped
Hi Sarbani, Use tpbconv. You can only (properly) restart from a point where you have a frame with velocities (in the .trr file) and preferrably energies (.edr). Best, Tsjerk On 8 Oct 2007 12:34:23 -, sarbani chattopadhyay < [EMAIL PROTECTED]> wrote: > > > hi, > I have been running a molecular dynamics simulation for 2 > nanoseconds.But it stopped in > the middle because of an internal problem.Is there any way to restart the > simulation from > the point it has stopped? > > Thank all > > Sarbani > > > > ___ > gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] only one cpu "works" in my linux cluster
Check the MPICH manuals for how to specify the nodes to run on. From memory, the option -machinefile lets you do this. - Original Message From: liu xin <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Monday, October 8, 2007 1:51:12 PM Subject: [gmx-users] only one cpu "works" in my linux cluster Dear GMXers this is how I've done it so far: grompp -f -c -p -o 12np.tpr -np 12 qsub -l node=6 12np.sh (/home/me/mpich2/bin/mpirun -np 12 mdrun -s 12np.tpr -np 12 ) then it seems my mdrun works fine, but when I ssh to each node to check the cpu efficiency with "top", I find that there's only one cpu works with 12 processes! The other nodes are completely idle. the cluster have 56 Intel Xeon duo 3.0G CPUs, below is my system info: Linux login 2.4.21-32.EL #1 SMP Fri Apr 15 21:02:58 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux our administrator have installed mpich1.2.7 in the default DIR (/usr/local), but I have some problems to do mpi-mdrun with mpich1.2.7, so I installed mpich2 in my personal dir. I've searched the list, but cant get any solution. Does it have something to do with the kernel or there's some conflict between mpich1 and 2, or something else? This is the first time I build up a Linux Cluster on my own, ANY suggestions are appreciated ! Xin Liu Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online. http://smallbusiness.yahoo.com/webhosting ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory
Dear Jeroen, I am using gromacs-3.2.1, and PME. Is that the problem? Yours Tanping --- van Bemmelen <[EMAIL PROTECTED]> wrote: > Hi Tanping, > > This may seem irrelevant, but are you using PME? And > which version of > GROMACS is it? > > Greetings, > Jeroen > > > >Date: Sun, 7 Oct 2007 08:46:04 -0700 (PDT) > >From: Tanping Li <[EMAIL PROTECTED]> > >Subject: Re: [gmx-users] Different nstxout and > nstvout in mdp file > > gives totally different trajectory > >To: Discussion list for GROMACS users > > >Message-ID: > <[EMAIL PROTECTED]> > >Content-Type: text/plain; charset=iso-8859-1 > > > >Dear Tsjerk, > > > >Thanks for your help. > > > >I run the two jobs on a cluster, maybe on different > nodes; > > > >After just a few hundreds ps, the coordinates of > the system > >differs a lot. When I calculate the distance > between two > >atoms, there is about 1.5A difference; > > > >Everything else in mdp file is exactly same. > > > > > >Yours > >Tanping > ___ > gmx-users mailing listgmx-users@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 > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] only one cpu "works" in my linux cluster
Dear GMXers this is how I've done it so far: grompp -f -c -p -o 12np.tpr -np 12 qsub -l node=6 12np.sh (/home/me/mpich2/bin/mpirun -np 12 mdrun -s 12np.tpr-np 12 ) then it seems my mdrun works fine, but when I ssh to each node to check the cpu efficiency with "top", I find that there's only one cpu works with 12 processes! The other nodes are completely idle. the cluster have 56 Intel Xeon duo 3.0G CPUs, below is my system info: Linux login 2.4.21-32.EL #1 SMP Fri Apr 15 21:02:58 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux our administrator have installed mpich1.2.7 in the default DIR (/usr/local), but I have some problems to do mpi-mdrun with mpich1.2.7, so I installed mpich2 in my personal dir. I've searched the list, but cant get any solution. Does it have something to do with the kernel or there's some conflict between mpich1 and 2, or something else? This is the first time I build up a Linux Cluster on my own, ANY suggestions are appreciated ! Xin Liu ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] restart md from the point it had stopped
hi, I have been running a molecular dynamics simulation for 2 nanoseconds.But it stopped in the middle because of an internal problem.Is there any way to restart the simulation from the point it has stopped? Thank all Sarbani___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gmx continuation run
Hi Vijaya, Did you note that tpbconv -extend extends the _remaining_ runtime with the amount given. So if the frame used for the continuation run had 140 ps remaining and you use -extend 5, you'll have 145 to go. Tsjerk On 10/8/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > vijaya subramanian wrote: > > Hi > > When I submit continuation runs with the following commands I find that > the the run is not extended for the time set by the tpbconv (5 ps) command > but an arbitrary time of 145 ps. > > > > tpbconv -s full3.tpr -f full3.trr -extend 5 -time 1150 -o full4tc.tpr > > What output do you get here? > > Mark > ___ > gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready
Hi, Adding a bit to Mark here... > I am reasonably certain that if I put in more than > > one copy of something which is in a .rtp file and _not_ in, say, > ions.itp, > > then it will be in both times in the .top file > > I think you are missing a point or two in comprehension here. The .rtp > file is a database used only by pdb2gmx to help construct a > correctly-connected topology for the residues in that database. I don't > know about the behaviour of pdb2gmx on a structure file with multiple > copies of the same molecule in different chains, but if it works, I > expect it won't notice the same molecule is the product, and would thus > produce two differently-named [ molecule ] sections for a dimeric > system. In any case, the OP did not need to have been using pdb2gmx, and > so the contents of the .rtp file are a red herring. This is of course very common with multimeric proteins, and Mark is right: pdb2gmx converts each chain it encounters to a "moleculetype". This has nothing to do with whatever is in the .rtp database. > (after all, two > > different-position glycines are in twice in the .top file...). > > pdb2gmx has atoms and residues as its two levels of structure. ...and a third level: chains (which are translated to moleculetypes and are a rough approximation of molecules). The topology file has atoms and molecules as its two levels of structure. In > the latter, residue names and numbers are retained purely for human > convenience, say, in constructing index groups. Since these glycine > residues are parts of molecules, they have to be replicated. This has > nothing to do with replication of molecules, however. You could define > multiple different [ molecule ] sections with different names for the > same molecule and then have multiple entries in the [ molecules ] > section, or you could have just one and have a single entry in the [ > molecules ] section. This brings us back to my original point that in > the latter case the numbering of the atoms in [ molecule ] sections does > not need to correspond to the structure file. > > Someone should definitely (re)read Chapter 5 of the manual... (and it's not Mark ;)). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
