Re: [gmx-users] error: Only triclinic boxes...
On 3/06/2011 3:06 AM, Elisabeth wrote:
Hello all,
I am getting the error below at the very beginning of the simulation
(both serial and parallel). I am sure I did not encounter this problem
before with the same input files. This has just happened now. I really
have no clue why this is happening. could you please help me? Thank
you all in advance.
You broke the simulation. Do not use parinello-rahman for equilibration.
It's only good close to equilibrium, and can oscillate wildly under the
wrong conditions. Generate velocities on a structure whose density is
appropriate for the ensemble you're working with, equilibrate, then
compress in stages, very gently. I've lost track of the number of times
I've suggested people not just randomly apply some large pressure on
some random configuration and expect it to work.
Mark
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, 0.0e+00, 0.0e+00}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
;Run control
integrator = md
dt = 0.002
nsteps = 100 ;5000
nstcomm = 100
;Output control
nstenergy = 100
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 1000
;Neighbor searching
nstlist = 10
ns_type = grid
;Electrostatics/VdW
coulombtype = Shift
vdw-type= Shift
rcoulomb-switch = 0
rvdw-switch = 0.9 ;0
;Cut-offs
rlist = 1.25
rcoulomb= 1.0
rvdw= 1.0
;Temperature coupling
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
;Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 1
compressibility = 3.5e-5
ref_p = 10
;Velocity generation
gen_vel = yes
gen_temp= 300.0
gen_seed= 173529
;Bonds
constraints = all-bonds
constraint-algorithm = lincs
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Re: [gmx-users] option -pbc in trjconv
On 3/06/2011 3:42 PM, Kavyashree M wrote: Dear users, I wanted to ensure that the option of -pbc in trjconv is only for visualization, and if I do all possible calculations with the original .xtc file there wont be any problem. -pbc is for any purpose you can think of. Some analyses of periodic simulations only make sense for some representations of the unit cell. Some don't. Read about the tool, think carefully, then act :-) Mark -- gmx-users mailing listgmx-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
Re: [gmx-users] option -pbc in trjconv
Dear Sir, I used dodecahedron for the simulation. My specific doubt was whether do we need to modify the .xtc file using some options of -pbc like nojump, mol, before going for analysis or we can directly go for analysis using the raw .xtc file. Thanking you With regards M. Kavyashree -- Forwarded message -- From: Mark Abraham mark.abra...@anu.edu.au Date: Fri, Jun 3, 2011 at 12:58 PM Subject: Re: [gmx-users] option -pbc in trjconv To: Discussion list for GROMACS users gmx-users@gromacs.org On 3/06/2011 3:42 PM, Kavyashree M wrote: Dear users, I wanted to ensure that the option of -pbc in trjconv is only for visualization, and if I do all possible calculations with the original .xtc file there wont be any problem. -pbc is for any purpose you can think of. Some analyses of periodic simulations only make sense for some representations of the unit cell. Some don't. Read about the tool, think carefully, then act :-) Mark -- gmx-users mailing listgmx-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 -- Yours Sincerely, Dr. Shankar Prasad Kanaujia Research Associate C/O - Professor K. Sekar Bioinformatics Centre Indian Institute of Science, Bangalore-12 Phone: +919480258032 Office: +91-080-2293-3059 -- gmx-users mailing listgmx-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
Re: [gmx-users] option -pbc in trjconv
On 3/06/2011 6:48 PM, Kavyashree M wrote: Dear Sir, I used dodecahedron for the simulation. My specific doubt was whether do we need to modify the .xtc file using some options of -pbc like nojump, mol, before going for analysis or we can directly go for analysis using the raw .xtc file. Maybe. Only a general answer can be given to a general question. Mark Thanking you With regards M. Kavyashree -- Forwarded message -- From: *Mark Abraham* mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au Date: Fri, Jun 3, 2011 at 12:58 PM Subject: Re: [gmx-users] option -pbc in trjconv To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org On 3/06/2011 3:42 PM, Kavyashree M wrote: Dear users, I wanted to ensure that the option of -pbc in trjconv is only for visualization, and if I do all possible calculations with the original .xtc file there wont be any problem. -pbc is for any purpose you can think of. Some analyses of periodic simulations only make sense for some representations of the unit cell. Some don't. Read about the tool, think carefully, then act :-) Mark -- 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 -- Yours Sincerely, Dr. Shankar Prasad Kanaujia Research Associate C/O - Professor K. Sekar Bioinformatics Centre Indian Institute of Science, Bangalore-12 Phone: +919480258032 Office: +91-080-2293-3059 -- gmx-users mailing listgmx-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] strain
Hi Gromacs users, We would like to apply strain to the system. Is this possible to do with gromacs and if it is how? Thank you in advance, Deniz -- gmx-users mailing listgmx-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
Re: [gmx-users] Solvating dodecahedron
Hi Justin, Note that the pseudo-sphere representation is for visualization purposes only; the triclinic cell should be the input for any simulation. This not true. It doesn't matter which representation you use as input. Molecules may be broken over PBC, but the topological information is taken from the .tpr file anyway. Gromacs may spit out broken molecules, and will swallow them just as well. Groetjes, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-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
Re: [gmx-users] Solvating dodecahedron
Tsjerk Wassenaar wrote: Hi Justin, Note that the pseudo-sphere representation is for visualization purposes only; the triclinic cell should be the input for any simulation. This not true. It doesn't matter which representation you use as input. Molecules may be broken over PBC, but the topological information is taken from the .tpr file anyway. Gromacs may spit out broken molecules, and will swallow them just as well. Good to know, and that certainly makes sense. I guess I was thinking of an old post that warned never to do this; perhaps there was some problem with PBC handling in an older version, and thus I made a habit to never change the input coordinates. -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 listgmx-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] Combining part files after using -noappend
Hi all, I just discovered nohup for running my simulation without hangup. For some reason using nohup wouldn't except the checksum on my previous md.log file so I just added the -noappend option to create new files. I'm curious, is there a way to combine the part files that emerge from using the -noappend command? I.e. I would like to combine my original traj.xtc with the traj.part0001.xtc and similar for all the files (ener.edr, pullf.xvg, pullx.xvg and traj.trr). Thank so much for your time, Sincerely, Zack -- gmx-users mailing listgmx-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
Re: [gmx-users] Combining part files after using -noappend
Zack Scholl wrote: Hi all, I just discovered nohup for running my simulation without hangup. For some reason using nohup wouldn't except the checksum on my previous md.log file so I just added the -noappend option to create new files. I'm curious, is there a way to combine the part files that emerge from using the -noappend command? I.e. I would like to combine my original traj.xtc with the traj.part0001.xtc and similar for all the files (ener.edr, pullf.xvg, pullx.xvg and traj.trr). For .xtc and .trr files, use trjcat. For .edr files, use eneconv. For anything else, like your .xvg files, use Unix commands like cat. -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 listgmx-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
Re: [gmx-users] Is there still interest in rigid-body simulation?
Hi Justin, I added this feature as a new issue under the Gromacs project on Redmine. Recently I also added a Git fork with a very rudimentary version of rigid body code. Let me know if there is anything specific you think I should work on. Thanks a lot, Adam On Thu, Apr 7, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu wrote: It seems like lots of people are in favor of this idea. Since Gromacs is undergoing some MAJOR changes to its underlying code, features, etc in the coming months it would be prudent to: 1. Post this proposal as a project/enhancement request on redmine.gromacs.org (and then volunteer to work on it) 2. Post the idea, framework, time needed, etc to the gmx-developers list so you're reaching a target audience for such tasks 3. Coordinate your efforts with the core developers who are currently developing a pretty detailed roadmap of future development (much of this can be done on the redmine site) All of these will improve the chances of making useful code contributions that can eventually get incorporated into a release, or at least a git branch somewhere. -Justin Semen Esilevsky wrote: This would be very good! I'm working on somewhat similar thing, but I plan to use external library for computing rigid body forces from atom forces. If gromacs will be able to compute rigid body forces itself it will be great! Regards, Semen *From:* gyorgy.han...@fc.up.pt gyorgy.han...@fc.up.pt *To:* gmx-users@gromacs.org *Sent:* Thu, April 7, 2011 6:50:37 PM *Subject:* Re: [gmx-users] Is there still interest in rigid-body simulation? Hello, I think it would be very good to have this feature in gromacs. In fact I've recently had some problems with constraining some species in my simulations. Finally I've sorted out with shake but your solution seems to me less problematic. Thanks in advance. Best, Gyorgy Quoting ms deviceran...@gmail.com mailto:deviceran...@gmail.com: On 27/03/11 23:02, Adam Herbst wrote: Hi all, I have seen a few posts on gmx-users indicating a desire to treat certain atom groups as rigid bodies in MD simulations. I just started implementing this, and so far I have it working for translational forces (not rotation, though this should be simple to add), even when the group is split over multiple processors. At the moment I have the rigid body groups specified as freeze groups in the mdp file, but there could be a separate option. Would anyone else find this useful? The problem is that: (a) I am modifying GROMACS 4.5.1, so I am some months out of date, and (b) my code is probably not to spec. If it is worthwhile, I can restart from 4.5.4 (the code modifications are quite small) and make an effort to conform to coding standard. Best, Adam Herbst I would love that!! --Massimo Sandal, Ph.D. http://devicerandom.org --gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] gmx4.5.4 installation help
Add --with-pic when configuring fftw. -- Josh On Thu, 2011-06-02 at 15:16 +0800, Jianguo Li wrote: The error message already shows some hints. Try recompile FFTW with -fPIC. Jianguo __ From: Chandan Choudhury iitd...@gmail.com To: gmx-users gmx-users@gromacs.org Sent: Thursday, 2 June 2011 15:03:03 Subject: [gmx-users] gmx4.5.4 installation help Hello gmx-users, I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64. 1. I installed fftw 3.2.2 ./configure --prefix /soft/sudip/abc/execs/fftw/ --enable-single --enable-threads 2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file a) ./configure --prefix=/soft/sudip/abc/execs/gromacs/ execute successfully without any complain. b) make /usr/bin/ld: /soft/sudip/abc/execs/fftw/lib/libfftw3f.a(apiplan.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /soft/sudip/abc/execs/fftw/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make: *** [all-recursive] Error 1 shows problem. Couldnot understand the origin of problem. Kndly let me know if some information is missing. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-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 -- Joshua L. Phillips Ph.D. Candidate - School of Engineering University of California, Merced jphilli...@ucmerced.edu -- gmx-users mailing listgmx-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] FFT plan mismatch with mdrun_mpi
Hello, I'll first apologize in case that this is a common issue with an available solution, but I have a problem running mdrun_mpi on a rock cluster and there is no amount of searching that I can do to find information on this error (manual, online docs, general google search). Could someone point me in the right direction for documentations? The error is the following: Program mdrun_mpi, VERSION 4.5.4 Source code file: gmx_fft_fftw2.c, line: 494 Fatal error: FFT plan mismatch - bad plan or direction. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I'm trying to run a simple mdrun as per one of the tutorial online on 50 CPUs. I can provide more details, but I'm hoping that there is already an answer to this question somewhere. Regards, Christian -- gmx-users mailing listgmx-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
Re: [gmx-users] FFT plan mismatch with mdrun_mpi
On 4/06/2011 3:42 AM, Christian Blouin wrote: Hello, I'll first apologize in case that this is a common issue with an available solution, but I have a problem running mdrun_mpi on a rock cluster and there is no amount of searching that I can do to find information on this error (manual, online docs, general google search). Could someone point me in the right direction for documentations? The error is the following: Program mdrun_mpi, VERSION 4.5.4 Source code file: gmx_fft_fftw2.c, line: 494 Fatal error: FFT plan mismatch - bad plan or direction. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I've never seen this one before. I'm trying to run a simple mdrun as per one of the tutorial online on 50 CPUs. I can provide more details, but I'm hoping that there is already an answer to this question somewhere. I suspect most tutorials are based on systems that are too small to want to use this many processors. Parallelism is not a magic bullet that lets one run any calculation on any combination of processors. I'd suggest using fewer and hoping that solves the problem. Otherwise, trying linking with an up-to-date install of FFTW3. Mark -- gmx-users mailing listgmx-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] Re: my apologize
Eli:
It was a joke.
I want to clarify your relation to Moeed since he asked the SAME
question about the compression of the SAME polymer starting from the
spring of 2010, but never followed all our advices. Now, you start to
ask nearly the SAME questions about absolutely the SAME system. So, I
eventually wonder what the hell is going on.
Please, explore the archive of the mailing list to see all the remarks
devoted to your system. There is no sense to write the SAME things
once more. In the last case, your problem seems to be connected with a
bad input file (conf.gro). So, examine its content attentively and let
us know if this helped.
-
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
On Fri, Jun 3, 2011 at 3:11 PM, Elisabeth katesed...@gmail.com wrote:
Dear Justin,
I thank you cordially for all the help. To tell you the truth I did not mean
to complain. I just meant that the hints from gmx experts have not resolved
the problem yet. I am sure this must have been a misunderstanding. I am well
aware that you (or other experts) are helping on your own volition and there
is NO place to complain. I did not know I am violating the rules otherwise I
could simply wait for a few hours and send message from my own account. (Now
I see that it did not worth it)
At this point in time I can only say that I am awfully sorry for the mistake
I made. I do not know if you have removed my name form the list or not...I
know I deserve any punishment.
but apart from whatever punishment you are considering, please kindly do not
reply this message to the list (I am feeling guilty and publishing these
messages to the list makes me feel awkward).
Sorry to have sent you ( and Dr. Chaban) this message on your personal
account.
Best regards,
On 2 June 2011 22:40, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
Hello Dr. Vitaly Chaban,
Thank you. I asked a friend in our Dept. for help who is working on
different aspects of the more or less similar system. The message below was
sent on behalf of me. I apologize if I should not have done this. We thought
maybe it does not matter under which name messages are sent on the gmx list
and the idea of using mailing list is to share knowledge regardless of
names. I hope this has not offended you and other users.
I am also asking Justin to let me know if I have violated mailing list
rules. I make sure this will not happen again.
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
Having others send information around haphazardly to different individuals
and from colleagues or aliases just slows down your overall progress, since
we don't know who's getting (or providing) what information, or if the
discussions are even connected. Keep everything on the list and reply
directly to questions posed to you with as much detail as you can.
It's also not a good idea for anyone to complain that no one on the list
could help much. I had been trying to extract the necessary diagnostic
information from you, but perhaps not at the pace you'd like. Problems
aren't solved instantly, especially via email by people who have only a very
vague idea of what you're doing.
-Justin
Thank you,
Best regards,
On 2 June 2011 21:03, Vitaly Chaban vvcha...@gmail.com
mailto:vvcha...@gmail.com wrote:
Hey Eli:
What is the correlation observed between you and Moeed?
I suppose you eventually compressed your system so much, that it
became very distorted. Check your GRO file. I believe it is not
healthy inside.
Regards.
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
On Thu, Jun 2, 2011 at 6:53 PM, Moeed lecie...@googlemail.com
mailto:lecie...@googlemail.com wrote:
Dear Dr.Chaban,
I am so sorry to send you this message. Thank you for your
comments. I have
encountered a problem that no one on the list could help much. I
am very
hopeful you can assist me especially because I have noticed you
respond to
messages dealing with compression or NPT runs. I am really
confused since I
have been using the same input files (gro. top and mdp) and have
been
collecting without any problem. Since yesterday I am getting a
weird message
that is printed continuously until I kill mdrun.
arning: Only triclinic boxes with the first vector parallel to
the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
I have only polyethylene chains in my system. I really appreciate
if you
could help me or could kindly take a very brief look at my
[gmx-users] Why does the -append option exist?
At first, I thought the -append option of the mdrun command was great. However, I don't think it is anymore and have actually started questioning myself why it exists at the first place, and second, why has it become the default option in the newest versions? It is useless unless you run your simulations in a 100% safe from any unexpected problems (hardware, restarts, etc) mode, which is never the case. It is beyond me how such an option can become the default and how a statement like this: By default the output will be appending to the existing output files. The checkpoint file contains checksums of all output files, such that *you will never loose data when some output files are modified, corrupt or removed.* can be claimed without testing ALL of the scenarios that can lead to problems, that is, lost data. If one uses that option and the run is restarted and is again restarted before reaching the point of attempting to write a file, then things are lost, and most importantly, the most important piece of data, that being the trajectory file, could be completely lost! I don't know the code behind the checkpointing appending, but I can see how easy one can overwrite 100ns trajectories, for example, and obtain the same trajectories of size 0. Using the checkpoint capability appending make sense when many restarts are expected, but unfortunately it is exactly then when these options completely fail! As a new user of Gromacs, I must say I am disappointed, and would like to obtain an explanation of why the usage of these options is clearly stated to be safe when it is not, and why the append option is the default, and why at least a single warning has not been posted anywhere in the docs manuals? Thanks, Dimitar -- gmx-users mailing listgmx-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
Re: [gmx-users] Why does the -append option exist?
Well sometimes i run out of walltime when doing long simulations and append helps me not to do any file management after restarting simulations from the previous checkpoint. On Fri, Jun 3, 2011 at 3:26 PM, Dimitar Pachov dpac...@brandeis.edu wrote: At first, I thought the -append option of the mdrun command was great. However, I don't think it is anymore and have actually started questioning myself why it exists at the first place, and second, why has it become the default option in the newest versions? It is useless unless you run your simulations in a 100% safe from any unexpected problems (hardware, restarts, etc) mode, which is never the case. It is beyond me how such an option can become the default and how a statement like this: By default the output will be appending to the existing output files. The checkpoint file contains checksums of all output files, such that *you will never loose data when some output files are modified, corrupt or removed.* can be claimed without testing ALL of the scenarios that can lead to problems, that is, lost data. If one uses that option and the run is restarted and is again restarted before reaching the point of attempting to write a file, then things are lost, and most importantly, the most important piece of data, that being the trajectory file, could be completely lost! I don't know the code behind the checkpointing appending, but I can see how easy one can overwrite 100ns trajectories, for example, and obtain the same trajectories of size 0. Two restarts within a time frame where trajectory file is updated doesnt make sense. I really dont understand how you can loose trajectory files. Using the checkpoint capability appending make sense when many restarts are expected, but unfortunately it is exactly then when these options completely fail! How ? As a new user of Gromacs, I must say I am disappointed, and would like to obtain an explanation of why the usage of these options is clearly stated to be safe when it is not, and why the append option is the default, and why at least a single warning has not been posted anywhere in the docs manuals? Use -noappend Thanks, Dimitar -- gmx-users mailing listgmx-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 listgmx-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] g_rotacf
Hi, I have tried to use g_rotacf to get the rotational autocorrelation plot for a n-h vector, and I have two questions: 1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why? 2. The plot is bottom out at 500 ps and then go back up. What does it mean physically? Thanks for your insight. Simon -- gmx-users mailing listgmx-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
Re: [gmx-users] Why does the -append option exist?
On 4/06/2011 8:26 AM, Dimitar Pachov wrote: At first, I thought the -append option of the mdrun command was great. However, I don't think it is anymore and have actually started questioning myself why it exists at the first place, and second, why has it become the default option in the newest versions? It exists because it used to be a pain to manage your simulation file numbering. It is useless unless you run your simulations in a 100% safe from any unexpected problems (hardware, restarts, etc) mode, which is never the case. It is beyond me how such an option can become the default and how a statement like this: By default the output will be appending to the existing output files. The checkpoint file contains checksums of all output files, such that *you will never loose data when some output files are modified, corrupt or removed.* can be claimed without testing ALL of the scenarios that can lead to problems, that is, lost data. The checkpoint file records the position of the output file pointers at the time of the checkpoint, along with an MD5 checksum. Upon restarting with -append, mdrun seeks to that file pointer position, verifies the checksum and issues a fatal error if this is not possible. So if checkpoint and other files are not altered or removed after a crash, then the method seems pretty safe to me. The above text mentions you are safe even if you remove files - that's an overstatement. However, I can't see that removing a non-checkpoint file could lead to loss of useful data from other non-checkpoint files. If one uses that option and the run is restarted and is again restarted before reaching the point of attempting to write a file, then things are lost, If this is true, then it wants fixing, and fast, and will get it :-) However, it would be surprising for such a problem to exist and not have been reported up to now. This feature has been in the code for a year now, and while some minor issues have been fixed since the 4.5 release, it would surprise me greatly if your claim was true. You're saying the equivalent of the steps below can occur: 1. Simulation wanders along normally and writes a checkpoint at step 1003 2. Random crash happens at step 1106 3. An -append restart from the old .tpr and the recent .cpt file will restart from step 1003 4. Random crash happens at step 1059 5. Now a restart doesn't restart from step 1003, but some other step and most importantly, the most important piece of data, that being the trajectory file, could be completely lost! I don't know the code behind the checkpointing appending, but I can see how easy one can overwrite 100ns trajectories, for example, and obtain the same trajectories of size 0. I don't see how easy that is, without a concrete example, where user error is not possible. Using the checkpoint capability appending make sense when many restarts are expected, but unfortunately it is exactly then when these options completely fail! As a new user of Gromacs, I must say I am disappointed, and would like to obtain an explanation of why the usage of these options is clearly stated to be safe when it is not, and why the append option is the default, and why at least a single warning has not been posted anywhere in the docs manuals? I can understand and sympathize with your frustration if you've experienced the loss of a simulation. Do be careful when suggesting that others' actions are blame-worthy, however. The developers all act in good faith on a largely volunteer basis. Errors in coding do happen, and they do get attention as developers' time permits. However, developers' time rarely permits addressing feature X doesn't work, why not? in a productive way. Solving bugs can be hard, but will be easier (and solved faster!) if the user who thinks a problem exists follows good procedure. See http://www.chiark.greenend.org.uk/~sgtatham/bugs.html http://www.chiark.greenend.org.uk/%7Esgtatham/bugs.html Mark -- gmx-users mailing listgmx-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
Re: [gmx-users] g_rotacf
On 4/06/2011 9:02 AM, simon sham wrote: Hi, I have tried to use g_rotacf to get the rotational autocorrelation plot for a n-h vector, and I have two questions: 1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why? This can be normal for computed correlation functions. See chapter 5. (If you'd provided your command line, and information about how often you'd saved data, then I wouldn't be wasting our time with guesses...) Mark 2. The plot is bottom out at 500 ps and then go back up. What does it mean physically? Thanks for your insight. Simon -- gmx-users mailing listgmx-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
Re: [gmx-users] g_rotacf
On 4/06/2011 11:27 AM, Mark Abraham wrote: On 4/06/2011 9:02 AM, simon sham wrote: Hi, I have tried to use g_rotacf to get the rotational autocorrelation plot for a n-h vector, and I have two questions: 1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why? This can be normal for computed correlation functions. See chapter 5. Sorry, manual section 8.5. Mark (If you'd provided your command line, and information about how often you'd saved data, then I wouldn't be wasting our time with guesses...) Mark 2. The plot is bottom out at 500 ps and then go back up. What does it mean physically? Thanks for your insight. Simon -- gmx-users mailing listgmx-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] g_rdf problem
Hi, I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function of scattering vectors(q) using g_rdf -sq command . But, I found that there is no way that one can increase/decrease the grid spacing for structure factor calculation. I tried using -bin option , but that does not change anything as that only works for changing bin-width for Radial distribution functioncalculation. If some one can point me out any way out of changing the grid spacing for structure factor, that will be very helpful. Sanku-- gmx-users mailing listgmx-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] Re: Indexing problem when using genconf
Justin A. Lemkul wrote: Ryan S Davis (rsdavis1) wrote: I wanted to copy a bilayer into a grid of 2x2x1 replicas. I used genconf and everything seemed to work fine exept that annoying feature that the command does not reorder the molecule types, so I end up with a .top file looking like this... 1 #include martini_v2.1.itp 2 #include martini_v2.0_lipids.itp 3 #include martini_v2.0_cholesterol.itp 4 5 [ system ] 6 CHOL 7 8 [ molecules ] 9 DPPC 832 10 CHOL 208 11 W 8320 12 DPPC 832 13 CHOL 208 14 W 8320 15 DPPC 832 16 CHOL 208 17 W 8320 18 DPPC 832 19 CHOL 208 20 W 8320 Anyway, I run the simulation...no errors. I make an ndx file using make_ndx...indices look fine despite the repetitive order. HOWEVER, when I try to run commands such as trjconv with the index file as input, it reads all the way up to the first block of Waters and quits with the error Program trjconv, VERSION 4.0.7 Source code file: gmx_trjconv.c, line: 1037 Fatal error: Index[29952] 46593 is larger than the number of atoms in the trajectory file (46592) which I didnt expect, but makes perfect sense knowing that I specified in the .mdp file to not output water to the xtc file... xtc-grps = dppc chol Normally this isnt an issue because waters are typically last in the topology. But, I still need access to this data. How can I force the post-processing commands to read past the absent water blocks? The only options I see at the moments is to 1) scrap genconf, make new topology somehow, and rerun 2) reset to output water, and rerun 3) limit my analysis to the very sparse output from the .trr file I see two viable options, one of which is to use your option 1 via a few standard Unix tools to create a proper coordinate file, i.e.: grep DPPC conf.gro dppc grep CHOL conf.gro chol grep W conf.gro w cat dppc chol w system.gro Add a title, number of atoms, and box vectors at the end, and you're done. Then sum up the entries in [molecules] and the system should run just fine. The second option is to just create a dummy system that has only DPPC and CHOL molecules. Take your input coordinate file, strip out the waters, and renumber with genconf. Remove all W blocks from the .top and create a new .tpr file. This should now match the number of atoms in the trajectory and the order in which they appear. ...or just do this all in one step with tpbconv. I always manage to quickly think of the hardest way to do things :) -Justin Thanks, got it working with tpbconv. It would be nice to have an option on genconf to reorder the molecule types in the output... Not that I am willing to make that modification myself, ha :) Ryan-- gmx-users mailing listgmx-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
Re: [gmx-users] gmx4.5.4 installation help
Thanks everyone. It helped me in installation. -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Jun 3, 2011 at 10:36 PM, Joshua L. Phillips jphilli...@ucmerced.edu wrote: Add --with-pic when configuring fftw. -- Josh On Thu, 2011-06-02 at 15:16 +0800, Jianguo Li wrote: The error message already shows some hints. Try recompile FFTW with -fPIC. Jianguo __ From: Chandan Choudhury iitd...@gmail.com To: gmx-users gmx-users@gromacs.org Sent: Thursday, 2 June 2011 15:03:03 Subject: [gmx-users] gmx4.5.4 installation help Hello gmx-users, I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64. 1. I installed fftw 3.2.2 ./configure --prefix /soft/sudip/abc/execs/fftw/ --enable-single --enable-threads 2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file a) ./configure --prefix=/soft/sudip/abc/execs/gromacs/ execute successfully without any complain. b) make /usr/bin/ld: /soft/sudip/abc/execs/fftw/lib/libfftw3f.a(apiplan.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /soft/sudip/abc/execs/fftw/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make: *** [all-recursive] Error 1 shows problem. Couldnot understand the origin of problem. Kndly let me know if some information is missing. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-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 -- Joshua L. Phillips Ph.D. Candidate - School of Engineering University of California, Merced jphilli...@ucmerced.edu -- gmx-users mailing listgmx-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 listgmx-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
