Re: 回复： Re: [gmx-users] how to remd an alysi?
xi zhao wrote: > I performed remd using GROMACS 3.3.1 at four different temperatures: > 270k, 400k, 540k, 660k, and produced four trajectories. I want to know > whether my simulation is ok, but I do not know how to analysis my > trajectories. Probably these temperatures are spaced far too widely if you are not doing a vacuum simulation of a small peptide. Check literature for more suitable temperature ranges. > Though I have demux.pl script and produced > replica_index.xvg and replica_temp.xvg files, the contents of two files > are the same! I'm not familiar with the contents of theses files, but if your temperatures are too widely spaced, you won't see exchanges, and that might be the reason for these files being identical. > I use trjcat_d to produce a continuous > trajectory,according to wiki gromacs. In fact, for a REMD > simulation, I can not judge whether the simulations is ok , and if they > are ok, how to further analyze or extract useful information from > trajectories! Are you clear? This question is common to all other MD simulations, and the answer to it depends on the purpose for the calculations. To get some ideas, have a look at the literature for similar calculations, do background reading and be prepared to think hard. 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] about DMSO c-c bond and c-o bond in ffg53a6 force field
wang kelvin wrote: Hi, everyone. I am simulating DMSO. At fisrst ,bond parameters contain two c-c bonds,and c-o bond ,which actually not in existence. But gmx 's force field ffg53a6 documents in top directory defines these bonds. When running mdrun , system reminds "segmentation default". then i get these virtual bond away , since that mdrun is ok ! Can anyone tell me why gmx define these bonds (ie. C-O bond ,C-C bond)? And has eliminating these bonds effects on simulating result? Any suggestion is appreciated. I'd suggest describing your observations more coherently and in more detail. Otherwise, with a view to using SHAKE, some united-atom DMSO models prefer to define six bonded interactions, rather than three bonded interactions and three angle interactions. Thus, DMSO C-C and C-O interactions can exist. However, you should already know about this from reading the literature about your DMSO model, right? :-) 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] generation of amorphous surface
h a wrote: Dear users, I'm using Gromacs to generate polymer surface. Is it possible using genbox command ? As I see genbox is used to create a box filled with Correct. editconf can do basic replication of a periodic image, however. 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
[gmx-users] generation of amorphous surface
Dear users, I'm using Gromacs to generate polymer surface. Is it possible using genbox command ? As I see genbox is used to create a box filled with solvent. thank you, Sincerely Harshith ___ 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] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)
Dear Justin, The reply is below: I am doing a simulation of a carbon nanotube (CNT) inside water. First I am going to describe my problem and then give info about my simulation setup (initial conditions, parameters, etc.). My problem is as follows: (1) I am doing a *.gro file of a *.pdb of a (16,16) CNT, without using pdb2gmx, that is with my own code. I also add manually velocity columns (vx, vy, vz) = (0, 0, 0) to the *.gro file. It works properly, since VMD and various gromacs commands can process the *.gro file. (2) Then, I use editconf in order to center the nanotube and set up a rectangular box. There, when I give a finite velocity (just to check) to every carbon (C) atom in CNT , such as (vx, vy, vz) = (0.0001, 0.0001, 0.0001) for every C, then editconf preserves the velocity info and includen in the output *.gro file. In fact I should fix the position of the nanotube. But when (vx, vy, vz) = (0, 0, 0), then it says "cannot find velocity information" or something like that and ignores the velocity columns. Telling us "or something like that" does not make it easy for us to help you. What was your exact command line input, and what was the exact message? Likely it stems from using velocities of 0, 0, 0. The .gro format is fixed: http://www.gromacs.org/documentation/reference/online/gro.html My command line input is: editconf -f CNT1616_L50_1.gro -o CNT1616_50_wbox.gro -box 8.0 6.0 6.0 -c The output is: ... Read 1280 atoms Volume: 125 nm^3, corresponds to roughly 56200 electrons No velocities found system size : 4.920 2.170 2.170 (nm) center : 0.000 -0.000 0.000 (nm) box vectors : 5.000 5.000 5.000 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 125.00 (nm^3) shift : 4.000 3.000 3.000 (nm) new center : 4.000 3.000 3.000 (nm) new box vectors : 8.000 6.000 6.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 288.00 (nm^3) ... That is, the message is "No velocities found". Note that editconf succeeds, so "No velocities found" is not an error. To be more clear (as you suggested) : My gro file is as follows: Carbon Nanotube 1280 1 CNT C11 -2.460 0.603 0.902 0.000 0.000 0.000 1 CNT C22 -2.337 0.661 0.861 0.000 0.000 0.000 1 CNT C33 -2.460 0.902 0.603 0.000 0.000 0.000 1 CNT C44 -2.337 0.940 0.542 0.000 0.000 0.000 1 CNT C55 -2.460 1.064 0.212 0.000 0.000 0.000 1 CNT C66 -2.337 1.076 0.142 0.000 0.000 0.000 1 CNT C77 -2.460 1.064 -0.212 0.000 0.000 0.000 1 CNT C88 -2.337 1.048 -0.281 0.000 0.000 0.000 1 CNT C99 -2.460 0.902 -0.603 0.000 0.000 0.000 1 CNT C10 10 -2.337 0.861 -0.661 0.000 0.000 0.000 ... There is no problem with gro format. This is why I wrote " It works properly, since VMD and various gromacs commands can process the *.gro file" in my previous message. (3) So, after that, when I use genbox in order to fill the box with water, than all the velocity information disappears, no matter whether the initial velocity for C atoms are finite or simply 0. The gro file includes the coordinates of both CNT and H2O molecules, but there is no velocity info! See genbox -h for why this happens. (4) Then I run grompp with my output *.gro file, *.top (topology) file and *.mdp file which I will describe the settings below, in order to produce a *.tpr file. When I read the resulting *.tpr file with gmxdump, again there are just coordinates, no velocity columns. Probably because you have gen_vel = no, and there are no velocities in the input file (see above). Then how does the simulation calculate the equations of motion? As it is obvious from physics and from the gromacs manual, the initial velocities should be set to zero by default by the program. (5) I do an energy minimisation step, I check the output (both the *.trr file and *.gro file) again there is no velocity info. As there shouldn't be, for an energy minimization. (6)After that, again I modify my *.mdp file in order to do MD, I run grompp just as before, than mdrun, and there is no velocity info both in *.trr and *.xtc files, even if nvout=positive integer and gen_vel=yes (when it is set to be"no", then again there should be velocity info in the following time steps). I also tried to put to input *.gro file velocity columns by hand, but it didn't work. What didn't work? Again, be more specific. What were your commands, and what output did you receive? Your .mdp file looks fine with respect to velocity generation and output parameters. Does the simulation run to completion? "It didn't work" == "there is no velocity info both in *.trr and *.xtc files, even if nvout=positive integer and gen_vel=yes" The simulation was complete, and it was pretty succesful, I was able to
Re: [gmx-users] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)
Dear Mark, I am doing a simulation of a carbon nanotube (CNT) inside water. First I am going to describe my problem and then give info about my simulation setup (initial conditions, parameters, etc.). My problem is as follows: (1) I am doing a *.gro file of a *.pdb of a (16,16) CNT, without using pdb2gmx, that is with my own code. I also add manually velocity columns (vx, vy, vz) = (0, 0, 0) to the *.gro file. It works properly, since VMD and various gromacs commands can process the *.gro file. This doesn't serve a purpose that I can see. (2) Then, I use editconf in order to center the nanotube and set up a rectangular box. There, when I give a finite velocity (just to check) to every carbon (C) atom in CNT , such as (vx, vy, vz) = (0.0001, 0.0001, 0.0001) for every C, then editconf preserves the velocity info and includen in the output *.gro file. In fact I should fix the position of the nanotube. But when (vx, vy, vz) = (0, 0, 0), then it says "cannot find velocity information" or something like that and ignores the velocity columns. (3) So, after that, when I use genbox in order to fill the box with water, than all the velocity information disappears, no matter whether the initial velocity for C atoms are finite or simply 0. The gro file includes the coordinates of both CNT and H2O molecules, but there is no velocity info! Keeping them really doesn't serve a purpose - you've radically changed the system, so those old velocities can't be from a meaningful ensemble any more, even if they were to start with. I see. (4) Then I run grompp with my output *.gro file, *.top (topology) file and *.mdp file which I will describe the settings below, in order to produce a *.tpr file. When I read the resulting *.tpr file with gmxdump, again there are just coordinates, no velocity columns. With gen_vel = no then this should be expected. (5) I do an energy minimisation step, I check the output (both the *.trr file and *.gro file) again there is no velocity info. Since EM is mechanical, not dynamical, there are no velocities. (6)After that, again I modify my *.mdp file in order to do MD, I run grompp just as before, than mdrun, and there is no velocity info both in *.trr and *.xtc files, even if nvout=positive integer and gen_vel=yes (when it is set to be"no", then again there should be velocity info in the following time steps). You need 0 < *nstvout* to see velocity output. You won't see velocities in the .xtc file because that's not the purpose of the .xtc file. See http://wiki.gromacs.org/index.php/.xtc_file. IIRC the value of gen_vel is immaterial here, since the dynamics will start from zero velocities if you don't generate them. grompp will probably give you a warning about this, so make sure you check for them! mdrun will always write velocities at the final timestep, regardless of nstvout too. You will also need to change the integrator to md. OK, I see. But still there is no velocity output in the trr files. I checked the grompp output, it is as follows: checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours for CNT 1 Excluding 2 bonded neighbours for SOL 8962 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 17924 # ANGLES: 8962 initialising group options... processing index file... Analysing residue names: Opening library file /usr/share/gromacs/top/aminoacids.dat There are: 8963 OTHER residues There are: 0PROTEIN residues There are: 0DNA residues Analysing Other... Making dummy/rest group for Acceleration containing 1280 elements Making dummy/rest group for Freeze containing 26886 elements Making dummy/rest group for VCM containing 28166 elements Number of degrees of freedom in T-Coupling group CNT is 0.00 Number of degrees of freedom in T-Coupling group SOL is 80655.00 Making dummy/rest group for User1 containing 28166 elements Making dummy/rest group for User2 containing 28166 elements Making dummy/rest group for Or. Res. Fit containing 28166 elements Making dummy/rest group for QMMM containing 28166 elements T-Coupling has 2 element(s): CNT SOL Energy Mon. has 2 element(s): CNT SOL Acceleration has 2 element(s): SOL rest Freeze has 2 element(s): CNT rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): CNT Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest WARNING 1 [file aminoacids.dat, line 1]: Can not exclude the lattice Coulomb energy between energy groups Checking consistency between energy and charge groups... Net Acceleration in X direction, will be corrected Calculating fourier grid dimensions for X Y Z Using a fourier grid of 70x50x
[gmx-users] Error while running starting grompp and mdrun
Dear all, I get an error while running grompp or mdrun in a Sun cluster. Each node has 4 processors. I am submitting the job via a SGE script. After, I submit the job by "$qsub test_gromacs", the run terminates with the following message in the log file. Please tell me how to troubleshoot this problem. The error is repeated if the -np option is changed from 4 to 8. __ Fatal error: run input file topol.tpr was made for 4 nodes, while mdrun expected it to be for 1 nodes. [compute-1-30.local:24948] [0,0,0] ORTE_ERROR_LOG: Not found in file base/pls_base_proxy.c at line 189 __ The script is as follows: __ #!/bin/bash #$ -N mpich_gromacs #$ -S /bin/bash #$ -cwd #$ -j yDear all, I get an error while running grompp or mdrun in a Sun cluster. Each node has 4 processors. I am submitting the job via a SGE script. After, I submit the job by "$qsub test_gromacs", the run terminates with the following message in the log file. Please tell me how to troubleshoot this problem. The error is repeated if the -np option is changed from 4 to 8. Fatal error: run input file topol.tpr was made for 4 nodes, while mdrun expected it to be for 1 nodes. [compute-1-30.local:24948] [0,0,0] ORTE_ERROR_LOG: Not found in file base/pls_base_proxy.c at line 189 The script is as follows: #!/bin/bash #$ -N mpich_gromacs #$ -S /bin/bash #$ -cwd #$ -j y #Set the Parallel Environment and number of procs. #$ -pe mpich #Set the Parallel Environment and number of procs. #$ -pe mpich 4 #$ -l h_rt=01:00:00 echo Running on host `hostname` echo Directory is `pwd` echo This job runs on the following processors: cat $TMPDIR/machines | tee machinefile echo This job has allocated $NSLOTS processors export MDRUN=/home/raghu/gromacs/x86_64-unknown-linux-gnu/bin/mdrun export MPIRUN=/opt/mpich/gnu/bin/mpirun ##running directory cd /home/raghu/quad_md/case1 #add -v to create more verbose comments #-nice 0 needs to be before the -s and other arguments; this corrects the default of 19 (lowest priority) /home/raghu/gromacs/x86_64-unknown-linux-gnu/bin/grompp -f em.mdp -c box_sol.gro -p master.top -v -np 4 $MPIRUN -v -np 4 $MDRUN -v -nice 0 -np $NSLOTS -s topol.tpr -o traj.trr -e ener.edr -x traj.xtc -g md.log -c confout.gro >&em_run.log Regards, Ragothaman BMR - a key player in weight issues. Know more - http://in.search.yahoo.com/search?&fr=na_onnetwork_mail_taglines&ei=UTF-8&rd=r1&p=basal+metabolic+rate ___ 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] cannot print velocity information to trr/xtc files (Carbon Naotube inside water)
Nadir Kaplan wrote: What is going on here? How can I get velocity info? Any help will be greatly appreciated. Note that, there is an external acceleration on the water molecules, where is the position of CNT is fixed. So obviously water molecules should have finite velocities. Turn off the weird stuff (freeze groups and accelerate groups) until you've got your basic issues sorted out. MD simulations in general and CNT simulations in particular are not easy things to do right. Learn to walk before you try to run! :-) Freezing is for simplicity. One needs velocity to run. Yeah, but freezing and accelerating do things to velocities. If you're having problems, a good strategy is to simplify the situation until you can identify where the problem arises... thus, no freezing and accelerating. Below I paste another mdp file which I used for the MD part of the same simulation. That MD simulation was succesfully over and I was able to reproduce some results in the literature by using position info. Again, in the .trr file of that simulation, there are no velocities. Well, those reproduced results probably mean that there *were* velocities :-) Velocities must be there in the .trr for the last timestep, so long as mdrun was allowed to terminate normally. If you really had "nstvout = 5000" and you are looking at the correct non-post-processed trajectory with gmxdump on a suitable timestep, then your observations are inexplicable, unless there's some weird "gotcha" with no velocities being written for atoms in either a freeze or accelerate group... not that that makes much sense... In short, it seems much more likely you've made an error than that there's a weird bug. My earlier advice is still good - get a clean working directory and do the same kind of simulation but without the freeze and accelerate groups and see if you can reproduce your problem while recording everything you did on the way. If it now works, do the same but add in the weird stuff until you isolate the problem - if any. Good luck! 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] Error while running starting grompp and mdrun
Ragothaman Yennamalli wrote: Dear all, I get an error while running grompp or mdrun in a Sun cluster. Each node has 4 processors. I am submitting the job via a SGE script. After, I submit the job by "$qsub test_gromacs", the run terminates with the following message in the log file. Please tell me how to troubleshoot this problem. The error is repeated if the -np option is changed from 4 to 8. Since there's three different usages of -np you'd need to be more precise to make a good description of your problem. Fatal error: run input file topol.tpr was made for 4 nodes, while mdrun expected it to be for 1 nodes. [compute-1-30.local:24948] [0,0,0] ORTE_ERROR_LOG: Not found in file base/pls_base_proxy.c at line 189 The script is as follows: #!/bin/bash #$ -N mpich_gromacs #$ -S /bin/bash #$ -cwd #$ -j y #Set the Parallel Environment and number of procs. #$ -pe mpich #Set the Parallel Environment and number of procs. #$ -pe mpich 4 #$ -l h_rt=01:00:00 echo Running on host `hostname` echo Directory is `pwd` echo This job runs on the following processors: cat $TMPDIR/machines | tee machinefile echo This job has allocated $NSLOTS processors export MDRUN=/home/raghu/gromacs/x86_64-unknown-linux-gnu/bin/mdrun export MPIRUN=/opt/mpich/gnu/bin/mpirun ##running directory cd /home/raghu/quad_md/case1 #add -v to create more verbose comments #-nice 0 needs to be before the -s and other arguments; this corrects the default of 19 (lowest priority) /home/raghu/gromacs/x86_64-unknown-linux-gnu/bin/grompp -f em.mdp -c box_sol.gro -p master.top -v -np 4 $MPIRUN -v -np 4 $MDRUN -v -nice 0 -np $NSLOTS -s topol.tpr -o traj.trr -e ener.edr -x traj.xtc -g md.log -c confout.gro >&em_run.log The symptoms you observe make sense if $NSLOTS==1. Since all three -np flags need the same value after them, you should use the same variable each time. You should verify that the "echo" line tells you that has $NSLOTS==4 like you need. 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] Error while running starting grompp and mdrun
Dear Mark, Thanks for the mail. > > Since there's three different usages of -np you'd > need to be more > precise to make a good description of your problem. > I was changing the -np option in mdrun and grompp. > The symptoms you observe make sense if $NSLOTS==1. Since > all three -np > flags need the same value after them, you should use the > same variable > each time. You should verify that the "echo" line > tells you that has > $NSLOTS==4 like you need. > Yes. I checked by typing echo $NSLOTS and it says 4. So, I changed all the three -np option to -np $NSLOTS..Still the same error. Regards, Ragothaman Bollywood, fun, friendship, sports and more. You name it, we have it on http://in.promos.yahoo.com/groups/bestofyahoo/ ___ 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] Implicit Solvent Simulations
To the Gromacs user community, As of April 2007 it was not possible to do implicit solvent MDs with Gromacs (http://www.gromacs.org/pipermail/gmx-users/2007-April/026849.html). Has this changed since then? Kind regards, Una -- Una Bjarnadottir School of Biomolecular and Biomedical Science Conway Institute UCD Dublin 4, Ireland Phone: +353 1 716 6874, Fax: +353 1 716 6898 Email: [EMAIL PROTECTED] ___ 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] Implicit Solvent Simulations
Hello Una (and everyone else) I'm happy to announce that, while not yet available in cvs, it will very soon be possible to do implicit solvation with Gromacs. I'm have a working implementation almost finished, and are currently running some tests to assure that the code is stable. With any luck we should be able to commit this to cvs in the next month or so :-) Cheers /Per Larsson, PhD student in the Lindahl group 22 maj 2008 kl. 16.13 skrev Una Bjarnadottir: To the Gromacs user community, As of April 2007 it was not possible to do implicit solvent MDs with Gromacs (http://www.gromacs.org/pipermail/gmx-users/2007-April/026849.html). Has this changed since then? Kind regards, Una -- Una Bjarnadottir School of Biomolecular and Biomedical Science Conway Institute UCD Dublin 4, Ireland Phone: +353 1 716 6874, Fax: +353 1 716 6898 Email: [EMAIL PROTECTED] ___ 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] Force field parameters in water or in vacuum?
Hi For one molecule, will Gromacs give the same set of force field parameters to this molecule no matter this molecule is put in water or in vacuum? The bond length, the bond angle, and the dihedral angles of the same molecule will be different in water and in vacuum. So, will the force field parameters be changed/ adjusted in water than in vacuum? How does Gromacs set the force field parameters for the molecule? I mean. are the force field paramters determined in local or in global? Could I change parts of the force field parameters which I found from the published paper? Or, I could not change parts of the force field parameters; instead, I have to change the whole set of the force field parameters??? Thank you Lin ___ 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] Force field parameters in water or in vacuum?
Quoting Chih-Ying Lin <[EMAIL PROTECTED]>: > Hi > For one molecule, will Gromacs give the same set of force field > parameters to this molecule no matter this molecule is put in water or > in vacuum? Depending on what's defined within the specific force field, yes. For example, ffG43b1 is a "vacuum forcefield," whereas most others are parameterized for use with condensed phases. > The bond length, the bond angle, and the dihedral angles of the same > molecule will be different in water and in vacuum. > So, will the force field parameters be changed/ adjusted in water than > in vacuum? There's no decision structure that Gromacs will magically use to determine what's in your system. All the parameters are pre-defined in the relevant .rtp and .itp files in $GMXLIB/top. > > > How does Gromacs set the force field parameters for the molecule? > I mean. are the force field paramters determined in local or in global? > Could I change parts of the force field parameters which I found from > the published paper? The location of your files will depend on how Gromacs was installed, but can always be found in $GMXLIB/top. If you want to make changes to an existing set of parameters, it is best to copy the relevant .rtp, .itp, etc. files into your working directory and alter then there. > Or, I could not change parts of the force field parameters; instead, I > have to change the whole set of the force field > parameters??? Well, I wouldn't make random changes to things :-) The changes you make have to be compatible with the functional form and derivation of the force field. Otherwise, anything you do would probably be somewhat questionable. -Justin > > > Thank you > Lin > ___ > 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 > Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ 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] Unable to minimize energy
This is likely an embarrassingly trivial problem, but let's see. I am following the energy minimization scheme presented in the groningen tutorial http://md.chem.rug.nl/education/mdcourse/MDpract.html I believe I follow the directions exactly, yet I can not minimize below Fmax~500 I download 1AKI, as in the tutorial, I issue pdb2gmx -f 1AKI.pdb grompp -f minim.mdp mdrun -v and I use the mdp file " title = Minimization of Hen Egg White Lysozyme (1AKI.pdb) ; Title of run ; The following lines tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor include = -I../top ; Directories to include in the topology format ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol nsteps = 200 ; Maximum number of (minimization) steps to perform nstenergy = 10; Write energies to disk every nstenergy steps nstxtcout = 10; Write coordinates to disk every nstxtcout steps xtc_grps= Protein ; Which coordinate group(s) to write to disk energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 5 ; Frequency to update the neighbor list and long range forces ns_type = simple; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = no; Periodic Boundary Conditions (yes/no)" I tried multiple choices of potentials and I tried gromacs 3.3.2, 3.3.3 and cvs, with single and double precision. They all finish with the same output(except single finishes in fewer steps) "Step= 57, Dmax= 3.2e-11 nm, Epot= -9.59522e+03 Fmax= 8.07834e+02, atom= 478 Step= 60, Dmax= 9.6e-12 nm, Epot= -9.59522e+03 Fmax= 8.07834e+02, atom= 478 Step= 62, Dmax= 5.8e-12 nm, Epot= -9.59522e+03 Fmax= 8.07834e+02, atom= 478 Step= 65, Dmax= 1.7e-12 nm, Epot= -9.59522e+03 Fmax= 8.07834e+02, atom= 478 Step= 67, Dmax= 1.0e-12 nm, Epot= -9.45085e+03 Fmax= 8.07834e+02, atom= 478 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1 writing lowest energy coordinates. Back Off! I just backed up confout.gro to ./#confout.gro.5# Steepest Descents converged to machine precision in 68 steps, but did not reach the requested Fmax < 1. Potential Energy = -9.59521978368287e+03 Maximum force = 8.07834306442108e+02 on atom 478 Norm of force = 1.49469417798063e+02 " This seems unreasonably high. Are there some obvious mistakes people make that result in this kind of behavior? I have tried multiple pdb structure and none of them can minimize below fmax~100. I have also tried l-bfgs and cg. None of them can converge to the request precision. thanks -Paul ___ 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] Force field parameters in water or in vacuum?
Chih-Ying Lin wrote: Hi For one molecule, will Gromacs give the same set of force field parameters to this molecule no matter this molecule is put in water or in vacuum? The bond length, the bond angle, and the dihedral angles of the same molecule will be different in water and in vacuum. So, will the force field parameters be changed/ adjusted in water than in vacuum? Assignment of force field parameters happens (e.g. by hand or with pdb2gmx) before it is possible to verify whether a solvent or vacuum simulation is intended. So you could do whatever you want and GROMACS isn't going to change things on you or prevent you from doing things... but probably most of these things aren't sensible. See http://wiki.gromacs.org/index.php/Force_Fields You should pick a force field that is known to work for the kind of calculation you want to do. How does Gromacs set the force field parameters for the molecule? In pdb2gmx, atoms in residues have their names matched to a database of residues (.rtp files), which then looks up the interactions in yet another database (.atp and .itp files). I mean. are the force field paramters determined in local or in global? I don't know what you mean. Could I change parts of the force field parameters which I found from the published paper? Yes, but this would be a very bad idea for someone starting their MD experience. See http://wiki.gromacs.org/index.php/Parameterization Or, I could not change parts of the force field parameters; instead, I have to change the whole set of the force field parameters??? Read carefully and choose something appropriate in advance, so that "changing" doesn't arise. 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] Error while running starting grompp and mdrun
Ragothaman Yennamalli wrote: Dear Mark, Thanks for the mail. Since there's three different usages of -np you'd need to be more precise to make a good description of your problem. I was changing the -np option in mdrun and grompp. The symptoms you observe make sense if $NSLOTS==1. Since all three -np flags need the same value after them, you should use the same variable each time. You should verify that the "echo" line tells you that has $NSLOTS==4 like you need. Yes. I checked by typing echo $NSLOTS and it says 4. It's the batch environment that matters, not your terminal environment. As I said last time, you'd need to look at the output from the batch script to verify its environment. So, I changed all the three -np option to -np $NSLOTS..Still the same error. That's not possible for any value of $NSLOTS. For troubleshooting, a (bash) script approach like command="mpirun -np $NSLOTS " echo $command `$command` will allow you to see in the standard output what you're actually doing, and so make a better description of the situation when emailing the list. 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] Unable to minimize energy
Paul Whitford wrote: This is likely an embarrassingly trivial problem, but let's see. I am following the energy minimization scheme presented in the groningen tutorial http://md.chem.rug.nl/education/mdcourse/MDpract.html I believe I follow the directions exactly, yet I can not minimize below Fmax~500 I did the tutorial as written and got "... Step= 115, Dmax= 1.3e-06 nm, Epot= -1.07212e+04 Fmax= 1.46265e+03, atom= 775 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 116 steps, but did not reach the requested Fmax < 1. Potential Energy = -1.0721238e+04 Maximum force = 1.5431615e+03 on atom 775 Norm of force = 9.6257832e+03" Thus I'd say you've done OK. Ultimately, if the EM prepares a structure well enough that the equilibration phase of the MD works, then that's good enough. 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] how to edit pdb file
Hi Justin, This command is just what I wanted. Thanks a lot. Hi Yang,Andrea and Alan, Thanks for your help. The link for PDB format is very useful.And I think Xemacs will be helpful for future use. Best regards, xiupeng From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL PROTECTED] Sent: Wednesday, May 21, 2008 9:50 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] how to edit pdb file Quoting "Wei, Xiupeng" <[EMAIL PROTECTED]>: > Dear GMX users, > I have a basic question. I want to put two same box in x direction. > So I need increase the number of atoms and change their x coordinates,then > combine it with the original one. But the file created by Excel can't be > recoganized by gromacs. Is there any method in Gromacs to handle that? I also > used Matlab, but it can't read pdb file correctly. Thanks. genconf -nbox 2 1 1 > > Best regards, > xiupeng > ___ > 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 > Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ 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] Simulate the organic molecule => input / output error
Hi Does the Gromacs only recognize the residues in the pdb file? If they are not the standard amino acids in the library, Gromacs can't read, right??? Or, how does the Gromacs simulate the organic molecule? The command pdb2gmx could not produce the top and the gro file. Instead, it shows that " File input/output error: " Thanks Lin ___ 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] Simulate the organic molecule => input / output error
Chih-Ying Lin wrote: Hi Does the Gromacs only recognize the residues in the pdb file? No... but pdb2gmx will only build a topology in an automated fashion if the residues are present in its databases. If they are not the standard amino acids in the library, Gromacs can't read, right??? A force field can potentially simulate species that are not present in the GROMACS .rtp database for that force field. See http://wiki.gromacs.org/index.php/Force_Fields and the links thereon. You sound like you could benefit from some thorough reading of background material - like a textbook or the early chapters of the GROMACS manual. The donated time of users on this mailing list doesn't serve as a replacement for your time reading such reference material. Or, how does the Gromacs simulate the organic molecule? Chapter 5 of the GROMACS manual has a partial example here. The command pdb2gmx could not produce the top and the gro file. Instead, it shows that " File input/output error: " Well that means you made a file input/output error. You made another error in expecting us to guess what it was you did wrong. As I wrote here just yesterday to another user, you need to be much more specific to actually get useful help. See http://www.gromacs.org/pipermail/gmx-users/2008-May/034162.html 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
[gmx-users] Re: Force field parameters in water or in vacuum?
Hi for 45a3 force field, is it created in vacuum / in water or solution ? Justin said the most of the force field is defined as condensed phase ??? Do you mean the liquid phase / or in water phase ? Thanks Lin Message: 7 Date: Thu, 22 May 2008 13:13:37 -0400 From: "Justin A. Lemkul" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Force field parameters in water or in vacuum? To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 Quoting Chih-Ying Lin <[EMAIL PROTECTED]>: > Hi > For one molecule, will Gromacs give the same set of force field > parameters to this molecule no matter this molecule is put in water or > in vacuum? Depending on what's defined within the specific force field, yes. For example, ffG43b1 is a "vacuum forcefield," whereas most others are parameterized for use with condensed phases. > The bond length, the bond angle, and the dihedral angles of the same > molecule will be different in water and in vacuum. > So, will the force field parameters be changed/ adjusted in water than > in vacuum? There's no decision structure that Gromacs will magically use to determine what's in your system. All the parameters are pre-defined in the relevant .rtp and .itp files in $GMXLIB/top. > > > How does Gromacs set the force field parameters for the molecule? > I mean. are the force field paramters determined in local or in global? > Could I change parts of the force field parameters which I found from > the published paper? The location of your files will depend on how Gromacs was installed, but can always be found in $GMXLIB/top. If you want to make changes to an existing set of parameters, it is best to copy the relevant .rtp, .itp, etc. files into your working directory and alter then there. > Or, I could not change parts of the force field parameters; instead, I > have to change the whole set of the force field > parameters??? Well, I wouldn't make random changes to things :-) The changes you make have to be compatible with the functional form and derivation of the force field. Otherwise, anything you do would probably be somewhat questionable. -Justin > > > Thank you > Lin > ___ > 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 > Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ On 5/22/08, Chih-Ying Lin <[EMAIL PROTECTED]> wrote: > Hi > For one molecule, will Gromacs give the same set of force field > parameters to this molecule no matter this molecule is put in water or > in vacuum? > The bond length, the bond angle, and the dihedral angles of the same > molecule will be different in water and in vacuum. > So, will the force field parameters be changed/ adjusted in water than > in vacuum? > > > How does Gromacs set the force field parameters for the molecule? > I mean. are the force field paramters determined in local or in global? > Could I change parts of the force field parameters which I found from > the published paper? > Or, I could not change parts of the force field parameters; instead, I > have to change the whole set of the force field > parameters??? > > > Thank you > > Lin > ___ 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] Re: Force field parameters in water or in vacuum?
Chih-Ying Lin wrote: Hi for 45a3 force field, is it created in vacuum / in water or solution ? Justin said the most of the force field is defined as condensed phase ??? Do you mean the liquid phase / or in water phase ? Check the GROMACS manual for literature references for this and other force fields. There's no substitute for having read them. 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
[gmx-users] Force field parameters in water or in vacuum?
Please don't post to the users list and the developers list simultaneously with the same question. I think this is more appropriately a users list question. I guess if you also get a reply on the developers list then it pays to post to both, but the idea is to put it only in one space. Hi For one molecule, will Gromacs give the same set of force field parameters to this molecule no matter this molecule is put in water or in vacuum? The bond length, the bond angle, and the dihedral angles of the same molecule will be different in water and in vacuum. So, will the force field parameters be changed/ adjusted in water than in vacuum? The parameters themselves will be the same in water or in vacuum. However, the behaviour of a molecule will be entirely different in water or in vacuum since vacuum lacs the hydrophobic effect that falls out of water being in the system. The hydrophobic effect is, in my opinion, one of the great success stories of MD. On the other hand, proteins will change their structure much faster in vacuum since the friction is much less in that case. So if you are looking to generate structures for some other purpose without caring if the sampling itself is Boltzmann (e.g. generating structures for use with the ENSEMBLE program to characterize intrinsically unfolded proteins by Dr. Julie Forman-Kay) then in vacuuo may be the best way to go. How does Gromacs set the force field parameters for the molecule? Based on the forcefield that you choose in pdb2gmx I mean. are the force field paramters determined in local or in global? local Could I change parts of the force field parameters which I found from the published paper? You _could_, but then you would be doing something entirely new and you should explain everything in your publication. Or, I could not change parts of the force field parameters; instead, I have to change the whole set of the force field parameters??? I think nearly everyone that you talk to would say that by changing _any_ part of the ff parameters then you are de-facto changing _all_ of the ff parameters since it is one interconnected set. I personally am not convinced that this is always the case. For example, I am not convinced that protein ff parameters are in any way tied to DNA ff parameters, even if they are generated consistently. But this is a minority view any you are most secure if you consider a ff as a single unmodifiable entity. BTW your post did not give any hint at what you are trying to do. I am sure that you don't want to be scooped, but it is difficult to give any assistance when you do not say what your goal is. Chris. ___ ___ 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] Force field parameters in water or in vacuum?
[EMAIL PROTECTED] wrote: Please don't post to the users list and the developers list simultaneously with the same question. I think this is more appropriately a users list question. I guess if you also get a reply on the developers list then it pays to post to both, but the idea is to put it only in one space. Hi For one molecule, will Gromacs give the same set of force field parameters to this molecule no matter this molecule is put in water or in vacuum? The bond length, the bond angle, and the dihedral angles of the same molecule will be different in water and in vacuum. So, will the force field parameters be changed/ adjusted in water than in vacuum? The parameters themselves will be the same in water or in vacuum. However, the behaviour of a molecule will be entirely different in water or in vacuum since vacuum lacs the hydrophobic effect that falls out of water being in the system. The hydrophobic effect is, in my opinion, one of the great success stories of MD. On the other hand, proteins will change their structure much faster in vacuum since the friction is much less in that case. So if you are looking to generate structures for some other purpose without caring if the sampling itself is Boltzmann (e.g. generating structures for use with the ENSEMBLE program to characterize intrinsically unfolded proteins by Dr. Julie Forman-Kay) then in vacuuo may be the best way to go. Actually in our experience this is not the case. In vacuum the proteins collapse and do hardly move away from this structure. See Biochemistry 46 pp. 933-945 (2007) JPCB 111 pp. 13147-13150 (2007) JACS 129 pp. 6726-6735 (2007) Int. J. Mass Spectrom. 248 pp. 124-135 (2006) How does Gromacs set the force field parameters for the molecule? Based on the forcefield that you choose in pdb2gmx I mean. are the force field paramters determined in local or in global? local Could I change parts of the force field parameters which I found from the published paper? You _could_, but then you would be doing something entirely new and you should explain everything in your publication. Or, I could not change parts of the force field parameters; instead, I have to change the whole set of the force field parameters??? I think nearly everyone that you talk to would say that by changing _any_ part of the ff parameters then you are de-facto changing _all_ of the ff parameters since it is one interconnected set. I personally am not convinced that this is always the case. For example, I am not convinced that protein ff parameters are in any way tied to DNA ff parameters, even if they are generated consistently. But this is a minority view any you are most secure if you consider a ff as a single unmodifiable entity. BTW your post did not give any hint at what you are trying to do. I am sure that you don't want to be scooped, but it is difficult to give any assistance when you do not say what your goal is. Chris. ___ ___ 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 thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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
[gmx-users] announcement: Advanced Gromacs workshop in Goettingen September 24-26
Hi, As promised, there will be a second gromacs workshop this year. The workshop will be held at the Max Planck Institute for biophysical chemistry in Goettingen, Germany from 24 to 26 september. As in the previous workshop in Stanford, the idea is to bring together people experienced with MD and talk about various subjects, such as non-equilibrium simulations, parallelization, QM/MM, or interesting new algorithms that we might want to implement in the future. But these are just examples. There is again no cost for participation in the workshop, but you will have to cover your own travel, accommodation and meals. We have made a block reservation a a hotel nearby the institute to get you reasonable rates. You can find additional information and register for the workshop at: http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/goettingen2008.html Because the number of participants is limited to 30-35, it will be "first come - first-served". Best, Gerrit -- Gerrit Groenhof MPI biophysical chemistry Goettingen Germany http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/index.html ___ 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
