[gmx-users] mpi run
Dear GMX Users, I have a PC with 4 CPU, but the Gromacs only use one CPU. the command of mpiru works on linux; however, the command of mdrun_mpi does not work. Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4 Many thanks, Mahmoud -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mpi run
Hi Mahmoud, for anyone to be able to help you, you need to provide a lot more information, at least: - which mpi library are you using? - how did you compile and/or install Gromacs? - what commands do you use to run mdrun and what was the output of it? Best, Carsten On Jul 8, 2010, at 9:41 AM, nanogroup wrote: Dear GMX Users, I have a PC with 4 CPU, but the Gromacs only use one CPU. the command of mpiru works on linux; however, the command of mdrun_mpi does not work. Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4 Many thanks, Mahmoud -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96
Dear Mark Many thanks Chrysostomos --- Στις Πέμ., 08/07/10, ο/η Mark Abraham mark.abra...@anu.edu.au έγραψε: Από: Mark Abraham mark.abra...@anu.edu.au Θέμα: Re: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96 Προς: Discussion list for GROMACS users gmx-users@gromacs.org Ημερομηνία: Πέμπτη, 8 Ιούλιος 2010, 4:49 - Original Message - From: C. Batistakis cbat...@yahoo.gr Date: Wednesday, July 7, 2010 23:19 Subject: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96 To: gromacs gmx-users@gromacs.org Dear all I am trying to simulate Nitrile-Butadiene-Rubber, using the Gromos96 force field. Let the availability of suitable parameters choose the force field :-) I have difficulties in finding the correct parameters from the bon.itp file , in order to define the polymer in the .rtp file. A first port of call would have been the appropriate paper for the force field - which might have made clear whether or not nitrile parameters were likely to be found. Can someone suggest which parameters I shall choose in the following: In Bond-stretching parameters For: 1) Triple bond between Carbon and Nitrogen (gb_) 2) Double bond CH=CH (gb_) In Bond-angle bending parameters For: 1) CH2-CH=CH (ga_) 2) CH-C≡N (ga_) In Dihedral-angle type code For: 1) CH2-CH=CH-CH2 (gd_) 2) CH2-CH-C≡N (gd_) If these parameters do not exist in this force field, can you suggest me another one to use? As a first step, try grep nitrile *.atp to see which of the atom type databases have nitrile in them. AMBER forcefields are probably also OK, but you'll have to install them seperately. Mark -Ακολουθεί συνημμένο- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problems with g_wham
Thanks Chris and Justin I do get the output I want from grompp(below). The distance of 5.507 nm is the distance that I want to start with and I assume it is therefore the equilibrium distance for the harmonic potential. The COM distances from the simulations fluctuate around this value which is what I want, although my histogram is the wrong shape. Pull group natoms pbc atom distance at start reference at t=0 0 8442 1 84 126 5.507 5.507 Cheers Gavin chris.ne...@utoronto.ca wrote: I missed that pull_start = yes, sorry. So Gavin, your run should have stayed around the starting position. Make the histogram directly and you should get a better idea. Chris. -- original message -- To clarify, the tutorial sets pull_init1 = 0 because it is used in conjunction with pull_start = yes, in order to take the starting COM distance as the reference. Check the grompp output to verify that you're getting what you think you should be. Otherwise, you'd have to set pull_start = no and modify your .mdp file to reflect the proper value of pull_init1 for every window. -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/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/mailing_lists/users.php
RE: [gmx-users] mpi run
During your installation, if you use --program-suffix=_mpi, so the mdrun_mpi will work. I suggest you to check the nodes of the cluster, probably try pbsnodes, on a master node no job may be run. Note that I do not know much about your information, so the (guessing) suggestion maybe not fit for your problems, just cause I once confused about why mine 4cpus barely used before too. Best, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Carsten Kutzner [ckut...@gwdg.de] Sent: Thursday, July 08, 2010 4:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mpi run Hi Mahmoud, for anyone to be able to help you, you need to provide a lot more information, at least: - which mpi library are you using? - how did you compile and/or install Gromacs? - what commands do you use to run mdrun and what was the output of it? Best, Carsten On Jul 8, 2010, at 9:41 AM, nanogroup wrote: Dear GMX Users, I have a PC with 4 CPU, but the Gromacs only use one CPU. the command of mpiru works on linux; however, the command of mdrun_mpi does not work. Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4 Many thanks, Mahmoud -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory
Hi, you can check with ldd mdrun_mpi whether really all needed libraries were found. Is libimf.so in /opt/intel/fc/10.1.008/lib ? The intel compilers also come with files called iccvars.sh or ictvars.sh. If you do source /path/to/iccvars.sh everything should be set as needed. Check the Intel Compiler documentation. Carsten On Jul 8, 2010, at 10:52 AM, zhongjin wrote: Dear users, When I am using GROMACS 4.0.7 on the Compute node ，executing command: mpiexec -n 4 mdrun_mpi -deffnm SWNT66nvt /dev/null and then met a problem :mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory but I have added export LD_LIBRARY_PATH=/opt/intel/fc/10.1.008/lib in the .bash_profile, the libimf.so is in this directory. However,when executing command:mdrun -deffnm SWNT66nvt ，it's OK ! Anybody could help me? Thanks a lot! Zhongjin He -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory
- Original Message - From: zhongjin zhongjin1...@yahoo.com.cn Date: Thursday, July 8, 2010 18:53 Subject: [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory To: gmx-users@gromacs.org --- | Dear users, When I am using GROMACS 4.0.7 on the Compute node ，executing command: mpiexec -n 4 mdrun_mpi -deffnm SWNT66nvt /dev/null and then met a problem :mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory but I have added export LD_LIBRARY_PATH=/opt/intel/fc/10.1.008/lib in the .bash_profile, the libimf.so is in this directory. However,when executing command:mdrun -deffnm SWNT66nvt ，it's OK ! Anybody could help me? Thanks a lot! Looks like the either MPI compiler is doing things differently from the normal compiler, or your execution environment does not have access to that /opt path, or even the environment variable. Consider also the use of LD_RUN_PATH - see compiler docs. It also might help to use gcc as the underlying compiler for mpicc - it's about the same as Intel - but that depends on what the underlying problem is. 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/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/mailing_lists/users.php
Re: RE: [gmx-users] mpi run
- Original Message -
From: #ZHAO LINA# zhao0...@e.ntu.edu.sg
Date: Thursday, July 8, 2010 18:53
Subject: RE: [gmx-users] mpi run
To: Discussion list for GROMACS users gmx-users@gromacs.org
P {margin-top:0;margin-bottom:0;}
---
|
During your installation, if you use --program-suffix=_mpi, so the mdrun_mpi
will work.
--program-suffix merely appends that suffix. --enable-mpi is necessary to
actually create MPI-enable mdrun. It is normal to use both of them together.
Mark
I suggest you to check the nodes of the cluster, probably try pbsnodes, on a
master node no job may be run.
Note that I do not know much about your information, so the (guessing)
suggestion maybe not fit for your problems, just cause I once confused about
why mine 4cpus barely used before too.
Best,
lina
---
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of Carsten Kutzner [ckut...@gwdg.de]
Sent: Thursday, July 08, 2010 4:04 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mpi run
Hi Mahmoud,
for anyone to be able to help you, you need to provide a lot more
information, at least: - which mpi library are you using? - how did you
compile and/or install Gromacs? - what commands do you use to run mdrun and
what was the output of it?
Best,Carsten
On Jul 8, 2010, at 9:41 AM, nanogroup wrote:
---
| Dear GMX Users,
I have a PC with 4 CPU, but the Gromacs only use one CPU.
the command of mpiru works on linux; however, the command of mdrun_mpi does
not work.
Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4
Many thanks,
Mahmoud
|
---
--
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-- Dr. Carsten Kutzner Max Planck Institute for Biophysical
Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077
Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
|
---
--
gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Compiling problems on MacOS X 10.6.4
Hi, Please post the output of the following commands: nm -arch i386 /opt/local/lib/libxml2.a | head nm -arch x86_64 /opt/local/lib/libxml2.a | head and in the directory where you typed make: file src/*/*.o | head Rui Rodrigues -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problems with g_wham
Have you watched the trajectory? That will show you what your pull group is doing. Is this a periodicity effect? It should be fairly obvious iff the sign of dX, etc flip-flops in the pullx.xvg file. -Justin Gavin Melaugh wrote: Thanks Chris and Justin I do get the output I want from grompp(below). The distance of 5.507 nm is the distance that I want to start with and I assume it is therefore the equilibrium distance for the harmonic potential. The COM distances from the simulations fluctuate around this value which is what I want, although my histogram is the wrong shape. Pull group natoms pbc atom distance at start reference at t=0 0 8442 1 84 126 5.507 5.507 Cheers Gavin chris.ne...@utoronto.ca wrote: I missed that pull_start = yes, sorry. So Gavin, your run should have stayed around the starting position. Make the histogram directly and you should get a better idea. Chris. -- original message -- To clarify, the tutorial sets pull_init1 = 0 because it is used in conjunction with pull_start = yes, in order to take the starting COM distance as the reference. Check the grompp output to verify that you're getting what you think you should be. Otherwise, you'd have to set pull_start = no and modify your .mdp file to reflect the proper value of pull_init1 for every window. -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/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/mailing_lists/users.php
[gmx-users] question about non-bonded parameters for CHARMM in GROMACS
Dear All, I am confused about the proper choice of non-bonded parameters for simulating the CHARMM force field in GROMACS. With other packages I use VDW-switch and PME with both VDW and the direct space coulomb cut-off at 1.2 and a neighbor-list cut-off of 1.4. The requirement in GROMACS that rlist=rcoulomb seems to make that parameter set impossible (unless one uses PME-switch, which is recommended against in the manual and not consistent with the original force field parameterization). I have seen a suggestion to use rvdw=rcoulomb=rlist=1.2, but grompp complains unless rlistrvdw under VDW-switch. That seems like a reasonable complaint, but I am new to GROMACS and wonder if I'm missing something. What is the recommended set of non-bonded parameters? Thanks in advance, Mike Hagan - Physics Department Brandeis University http://www.brandeis.edu/departments/physics/hagan/index.html - -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problems with g_wham
Hi Justin I am not using periodic boundary conditions for the simulations. I may have sorted it out now. I was generating velocities in the umbrella.mdp file, I have since set gen_vel = no, and the histogram has the correct shape (should this make a difference?) Cheers Gavin Justin A. Lemkul wrote: Have you watched the trajectory? That will show you what your pull group is doing. Is this a periodicity effect? It should be fairly obvious iff the sign of dX, etc flip-flops in the pullx.xvg file. -Justin Gavin Melaugh wrote: Thanks Chris and Justin I do get the output I want from grompp(below). The distance of 5.507 nm is the distance that I want to start with and I assume it is therefore the equilibrium distance for the harmonic potential. The COM distances from the simulations fluctuate around this value which is what I want, although my histogram is the wrong shape. Pull group natoms pbc atom distance at start reference at t=0 0 8442 1 84 126 5.507 5.507 Cheers Gavin chris.ne...@utoronto.ca wrote: I missed that pull_start = yes, sorry. So Gavin, your run should have stayed around the starting position. Make the histogram directly and you should get a better idea. Chris. -- original message -- To clarify, the tutorial sets pull_init1 = 0 because it is used in conjunction with pull_start = yes, in order to take the starting COM distance as the reference. Check the grompp output to verify that you're getting what you think you should be. Otherwise, you'd have to set pull_start = no and modify your .mdp file to reflect the proper value of pull_init1 for every window. -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/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/mailing_lists/users.php
Re: [gmx-users] problems with g_wham
Gavin Melaugh wrote: Hi Justin I am not using periodic boundary conditions for the simulations. I may have sorted it out now. I was generating velocities in the umbrella.mdp file, I have since set gen_vel = no, and the histogram has the correct shape (should this make a difference?) If you generate velocities without doing equilibration, then your system may not be at equilibrium and thus you are doing inaccurate sampling. Thus, if your system gets kicked in the wrong direction, the umbrella potential may have to fight to pull the desired group back to where it thinks it should be, might be overcompensating, etc. -Justin Cheers Gavin Justin A. Lemkul wrote: Have you watched the trajectory? That will show you what your pull group is doing. Is this a periodicity effect? It should be fairly obvious iff the sign of dX, etc flip-flops in the pullx.xvg file. -Justin Gavin Melaugh wrote: Thanks Chris and Justin I do get the output I want from grompp(below). The distance of 5.507 nm is the distance that I want to start with and I assume it is therefore the equilibrium distance for the harmonic potential. The COM distances from the simulations fluctuate around this value which is what I want, although my histogram is the wrong shape. Pull group natoms pbc atom distance at start reference at t=0 0 8442 1 84 126 5.507 5.507 Cheers Gavin chris.ne...@utoronto.ca wrote: I missed that pull_start = yes, sorry. So Gavin, your run should have stayed around the starting position. Make the histogram directly and you should get a better idea. Chris. -- original message -- To clarify, the tutorial sets pull_init1 = 0 because it is used in conjunction with pull_start = yes, in order to take the starting COM distance as the reference. Check the grompp output to verify that you're getting what you think you should be. Otherwise, you'd have to set pull_start = no and modify your .mdp file to reflect the proper value of pull_init1 for every window. -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/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/mailing_lists/users.php
Re: [gmx-users] problems with g_wham
Many thanks Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I am not using periodic boundary conditions for the simulations. I may have sorted it out now. I was generating velocities in the umbrella.mdp file, I have since set gen_vel = no, and the histogram has the correct shape (should this make a difference?) If you generate velocities without doing equilibration, then your system may not be at equilibrium and thus you are doing inaccurate sampling. Thus, if your system gets kicked in the wrong direction, the umbrella potential may have to fight to pull the desired group back to where it thinks it should be, might be overcompensating, etc. -Justin Cheers Gavin Justin A. Lemkul wrote: Have you watched the trajectory? That will show you what your pull group is doing. Is this a periodicity effect? It should be fairly obvious iff the sign of dX, etc flip-flops in the pullx.xvg file. -Justin Gavin Melaugh wrote: Thanks Chris and Justin I do get the output I want from grompp(below). The distance of 5.507 nm is the distance that I want to start with and I assume it is therefore the equilibrium distance for the harmonic potential. The COM distances from the simulations fluctuate around this value which is what I want, although my histogram is the wrong shape. Pull group natoms pbc atom distance at start reference at t=0 0 8442 1 84 126 5.507 5.507 Cheers Gavin chris.ne...@utoronto.ca wrote: I missed that pull_start = yes, sorry. So Gavin, your run should have stayed around the starting position. Make the histogram directly and you should get a better idea. Chris. -- original message -- To clarify, the tutorial sets pull_init1 = 0 because it is used in conjunction with pull_start = yes, in order to take the starting COM distance as the reference. Check the grompp output to verify that you're getting what you think you should be. Otherwise, you'd have to set pull_start = no and modify your .mdp file to reflect the proper value of pull_init1 for every window. -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/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/mailing_lists/users.php
RE: [gmx-users] Compiling problems on MacOS X 10.6.4
Thanks for your reply. The output from nm -arch i386 /opt/local/lib/libxml2.a | head is nm: file: /opt/local/lib/libxml2.a does not contain architecture: i386 and from nm -arch x86_64 /opt/local/lib/libxml2.a | head /opt/local/lib/libxml2.a(SAX.o): 3050 s EH_frame1 02a0 T _initdocbDefaultSAXHandler 30c8 S _initdocbDefaultSAXHandler.eh 0160 T _inithtmlDefaultSAXHandler 3098 S _inithtmlDefaultSAXHandler.eh T _initxmlDefaultSAXHandler 3068 S _initxmlDefaultSAXHandler.eh U _xmlParserError Best wishes George From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of J. Rui Rodrigues [joaquim.rodrig...@estg.ipleiria.pt] Sent: Thursday, July 08, 2010 5:57 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Compiling problems on MacOS X 10.6.4 Hi, Please post the output of the following commands: nm -arch i386 /opt/local/lib/libxml2.a | head nm -arch x86_64 /opt/local/lib/libxml2.a | head and in the directory where you typed make: file src/*/*.o | head Rui Rodrigues -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problems with g_wham
Depending on your system and chosen thermostat, gen-vel=no can be a dangerous idea (very small original velocities simply get scaled up); besides, you should be able to equilibrate from a gen-vel=yes pretty quickly. I don't disagree with Justin's comment, but just because it works doesn't mean its what you should do. I'd stick to an established procedure. Chris. -- original mesage -- Hi Justin I am not using periodic boundary conditions for the simulations. I may have sorted it out now. I was generating velocities in the umbrella.mdp file, I have since set gen_vel = no, and the histogram has the correct shape (should this make a difference?) Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problems with g_wham
O.K cheers Chris. I do intend to equilibrate the system at the desired temperature before constructing the histogram. chris.ne...@utoronto.ca wrote: Depending on your system and chosen thermostat, gen-vel=no can be a dangerous idea (very small original velocities simply get scaled up); besides, you should be able to equilibrate from a gen-vel=yes pretty quickly. I don't disagree with Justin's comment, but just because it works doesn't mean its what you should do. I'd stick to an established procedure. Chris. -- original mesage -- Hi Justin I am not using periodic boundary conditions for the simulations. I may have sorted it out now. I was generating velocities in the umbrella.mdp file, I have since set gen_vel = no, and the histogram has the correct shape (should this make a difference?) Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Compiling problems on MacOS X 10.6.4
Sorry, I forgot to post the output of file src/*/*.o | head src/gmxlib/3dview.o: Mach-O object i386 src/gmxlib/atomprop.o:Mach-O object i386 src/gmxlib/bondfree.o:Mach-O object i386 src/gmxlib/calcgrid.o:Mach-O object i386 src/gmxlib/calch.o: Mach-O object i386 src/gmxlib/chargegroup.o: Mach-O object i386 src/gmxlib/checkpoint.o: Mach-O object i386 src/gmxlib/cinvsqrtdata.o:Mach-O object i386 src/gmxlib/confio.o: Mach-O object i386 src/gmxlib/copyrite.o:Mach-O object i386 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of J. Rui Rodrigues [joaquim.rodrig...@estg.ipleiria.pt] Sent: Thursday, July 08, 2010 5:57 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Compiling problems on MacOS X 10.6.4 Hi, Please post the output of the following commands: nm -arch i386 /opt/local/lib/libxml2.a | head nm -arch x86_64 /opt/local/lib/libxml2.a | head and in the directory where you typed make: file src/*/*.o | head Rui Rodrigues -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Location of a molecule in a dodecahedron
Hi, I simulate a molecule in a dodecahedron. I used at the step with the editconf: editconf -f name.gro -o name.dod.pdb -bt dodecahedron -d 2.0 After my simulation I looked at the first frame and saw, that at two direction the molecule is actually 2 nm away of my edge, but the at the third edge the molecule is not in the middle, but near the edge. I looked also at the other pdb-files with the water before the simulation, and there the location of the molecule is the same, in my opinion not in the middle of the body. Is this a bug? Or have I done anything wrong? Thanks a lot for your helps! Greets, Birgit --- DI Birgit Hischenhuber Unit for Medical Statistics and Informatics Section for Biomedical Computersimulation and Bioinformatics Medical University of Vienna General Hospital Spitalgasse 23, BT88 A-1090 Vienna -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Location of a molecule in a dodecahedron
Birgit Hischenhuber wrote: Hi, I simulate a molecule in a dodecahedron. I used at the step with the editconf: editconf -f name.gro -o name.dod.pdb -bt dodecahedron -d 2.0 After my simulation I looked at the first frame and saw, that at two direction the molecule is actually 2 nm away of my edge, but the at the third edge the molecule is not in the middle, but near the edge. I looked also at the other pdb-files with the water before the simulation, and there the location of the molecule is the same, in my opinion not in the middle of the body. Is this a bug? Or have I done anything wrong? There is no bug. The representation is simply a triclinic cell, and probably periodicity effects. For visualization purposes only, you can correct the representation with trjconv -pbc mol -ur compact. -Justin Thanks a lot for your helps! Greets, Birgit --- DI Birgit Hischenhuber Unit for Medical Statistics and Informatics Section for Biomedical Computersimulation and Bioinformatics Medical University of Vienna General Hospital Spitalgasse 23, BT88 A-1090 Vienna -- 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/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/mailing_lists/users.php
RE: [gmx-users] Compiling problems on MacOS X 10.6.4
Hi, Looks like auto-detection for 64bit support on macs is not working with your machine. I had a similar problem some time ago on a Mac 10.5.8: http://lists.gromacs.org/pipermail/gmx-users/2010-April/050501.html As a workaround, you could pass the following flags to configure to see if it cures your problem: CFLAGS=-m64 -std=gnu99 -O3 Hope this helps, Rui Rodrigues On Thu, 8 Jul 2010 10:14:16 -0400, Patargias, George wrote Sorry, I forgot to post the output of file src/*/*.o | head src/gmxlib/3dview.o: Mach-O object i386 src/gmxlib/atomprop.o:Mach-O object i386 src/gmxlib/bondfree.o:Mach-O object i386 src/gmxlib/calcgrid.o:Mach-O object i386 src/gmxlib/calch.o: Mach-O object i386 src/gmxlib/chargegroup.o: Mach-O object i386 src/gmxlib/checkpoint.o: Mach-O object i386 src/gmxlib/cinvsqrtdata.o:Mach-O object i386 src/gmxlib/confio.o: Mach-O object i386 src/gmxlib/copyrite.o:Mach-O object i386 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of J. Rui Rodrigues [joaquim.rodrig...@estg.ipleiria.pt] Sent: Thursday, July 08, 2010 5:57 AM To: Discussion list for GROMACS users Subject: Re: [gmx- users] Compiling problems on MacOS X 10.6.4 Hi, Please post the output of the following commands: nm -arch i386 /opt/local/lib/libxml2.a | head nm -arch x86_64 /opt/local/lib/libxml2.a | head and in the directory where you typed make: file src/*/*.o | head Rui Rodrigues -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt) -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] P4_error for extending coarse grained MD simulations
Dear all, I have post this question about a two weeks ago. During these days, I followed suggestions from Mark and weixin, but did not fix it. Here, I repeat it again to seek more help. I attempt to extend MD simulation for a coarse-grained system. CG models are in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or 4.07. I tried to use check point file state.cpt to extend my simulation. The mdrun program can read to the check file. But it reported error like this: Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded with Money starting mdrun 'Protein in POPE bilayer' 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). step 1200, remaining runtime: 0 s p0_6991: p4_error: interrupt SIGSEGV: 11 I check the *state.cpt* file using *gmxdump* and compare it with other checkpoint files that can be used for extending All-atom simulations. I found that in the CG check point file, some sections are missing: *box-v (3x3)* and *thermostat-integral*. I am not sure whether this missing sections cause my run crash. If it is, could any one tell me possible reasons that result in the loss of box-v and thermostat-integral and how to fix the problem? Your suggestions are greatly helpful and appreciated. Justin Zhang 在 2010年6月25日 下午4:45，张春雷 chunleizhang@gmail.com写道： Information shown by gmxcheck: *Checking file state.cpt* # Atoms 9817 Last frame -1 time 36.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 *Checking file state_prev.cpt* # Atoms 9817 Last frame -1 time 359010.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 *Checking file md_360ns.trr* trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 # Atoms 9817 Reading frame2000 time 30.000 Item#frames Timestep (ps) Step 2401150 Time 2401150 Lambda2401150 Coords2401150 Velocities2401150 Forces 0 Box 2401150 Is anything wrong? 2010/6/25 Mark Abraham mark.abra...@anu.edu.au - Original Message - From: 张春雷 chunleizhang@gmail.com Date: Friday, June 25, 2010 16:46 Subject: Re: [gmx-users] P4_error for extending coarse grained MD simulations To: Discussion list for GROMACS users gmx-users@gromacs.org The last .gro file only provides coordinates of the system. No velocity is recorded. Actually, what I attempt to achieve is a binary identical trajectory. So I think the velocity from the last step is critical. I have tried another approach in which the checkpoint file is neglected. $mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g md_720ns.log It works. So the checkpoint file appears to contain some error. But it is generated by a normally finished production simulation. What does gmxcheck say about all the files involved? Mark Have you encountered similar things? Thank you for your suggestions! 在 2010年6月25日 上午9:16，weixin xwx...@gmail.com写道： How about using the last .gro file to continue your simulation? 2010/6/24 张春雷 chunleizhang@gmail.com Dear GMX-users, This is Justin. I am performing coarse-grained simulation on a protein-lipid bilayer system. This is a MARTINI CG model. I have successfully completed a 360ns simulation, during which the time step is 30 fs. I would like to extend the simulation to 1micro-second. The commands I used are: $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g md_360ns.log -cpi state.cpt However, I received the following message: Checkpoint file is from part 1, new output files will be suffixed part0002. Getting Loaded... Reading file md_720ns.tpr, VERSION 4.0.3 (double precision) Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded with Money starting mdrun 'Protein in POPE bilayer' 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). step 1200, remaining runtime: 0 s p0_6991: p4_error: interrupt SIGSEGV: 11 I have searched the mail-list, but found no similar report. I also search through google, but no answer seems satisfactory. I once performed extending simulation for all atom simulation, and the method mentioned above worked. Is anyone familiar with MARTINI CG simulation? Could you give me some suggestions? Many thanks! Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
RE: [gmx-users] Compiling problems on MacOS X 10.6.4
Yes, it did work. Thanks a lot! George From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of J. Rui Rodrigues [joaquim.rodrig...@estg.ipleiria.pt] Sent: Thursday, July 08, 2010 12:32 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] Compiling problems on MacOS X 10.6.4 Hi, Looks like auto-detection for 64bit support on macs is not working with your machine. I had a similar problem some time ago on a Mac 10.5.8: http://lists.gromacs.org/pipermail/gmx-users/2010-April/050501.html As a workaround, you could pass the following flags to configure to see if it cures your problem: CFLAGS=-m64 -std=gnu99 -O3 Hope this helps, Rui Rodrigues On Thu, 8 Jul 2010 10:14:16 -0400, Patargias, George wrote Sorry, I forgot to post the output of file src/*/*.o | head src/gmxlib/3dview.o: Mach-O object i386 src/gmxlib/atomprop.o:Mach-O object i386 src/gmxlib/bondfree.o:Mach-O object i386 src/gmxlib/calcgrid.o:Mach-O object i386 src/gmxlib/calch.o: Mach-O object i386 src/gmxlib/chargegroup.o: Mach-O object i386 src/gmxlib/checkpoint.o: Mach-O object i386 src/gmxlib/cinvsqrtdata.o:Mach-O object i386 src/gmxlib/confio.o: Mach-O object i386 src/gmxlib/copyrite.o:Mach-O object i386 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of J. Rui Rodrigues [joaquim.rodrig...@estg.ipleiria.pt] Sent: Thursday, July 08, 2010 5:57 AM To: Discussion list for GROMACS users Subject: Re: [gmx- users] Compiling problems on MacOS X 10.6.4 Hi, Please post the output of the following commands: nm -arch i386 /opt/local/lib/libxml2.a | head nm -arch x86_64 /opt/local/lib/libxml2.a | head and in the directory where you typed make: file src/*/*.o | head Rui Rodrigues -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt) -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] genbox and water model
Hi, I am using CHARMM forcefield with the tip3p. What input file(-cs) should i use to solvate the protein using the genbox command? The default is spc216.gro. What would be compatible with my system? I looked up the directory which has spc216.gro file. It has tip4p.gro file but for some reason doesnt have a tip3p.gro file. Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox and water model
Sai Pooja wrote: Hi, I am using CHARMM forcefield with the tip3p. What input file(-cs) should i use to solvate the protein using the genbox command? The default is spc216.gro. What would be compatible with my system? I looked up the directory which has spc216.gro file. It has tip4p.gro file but for some reason doesnt have a tip3p.gro file. http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file -Justin Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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/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/mailing_lists/users.php
[gmx-users] how to determine the box size
Hello Mark, Thank you for your reply. AS for the steps you mentioned to solvate a molecule: I have a simple molecule replicated by genconf -nbox in one direction. When I try to energy minimize this single molecule grompp em gives error: rlist is longer than half box size or longer than shortest diagnal boz size... I increase the size and everything is fine but can you please tell me what is the criterion to specify the size. Does boxsize affect results in MD? ( I am asking this because if I want to use genconf to replicate this molecule which is in a large boxzise the final size of the system can become very large so I have to use editconf to reduce the size again) Also sometimes some parts of the molcule in the box are outside the box when I see the trajectory (ngmx) at the beginning.. and I think because of the pbc it jups inthebox from the otherside. Should the particle be entirely in box at the beginning? Thanks, On 8 July 2010 01:47, Mark Abraham mark.abra...@anu.edu.au wrote: Please start new emails for new discussion topics. That way you increase the chance that people with the interest and expertise can use their time efficiently, and that you get an answer. Also, archives work better if you separate topics. Please Let me ask two more simple questions about solvating a molecule. I am using genbox to solvate a solute. I have solute.gro and solvent.gro. What should be the dimension of box in solvent.gro if i want to put -nmol numbers in the solute box. Does it matter what size the box of solvent is (last line in gro)? I don't think you are using the right tool for your problem, but your description is so opaque it's hard to tell. genbox -nmol will try to fill interstices, which need to exist for it to do any good. That means you need to have prepared your solvent.gro with your solute in mind. I have solvated the solute with 50 moleecules of solvent. I have the structure file obtained from genbox. To run em or MD I need to have top file. so I am using pdb2gmx and I get a top file for the solute and 50 solvents but I have one moleculetype (named protein by default). I am confused If I need to have 2 molecuels types for solute and solvent, also if I need to enter the number of solvent molecules at the end of the top file [mols] option, or what I have now is fine and I can proceed to em and md usuing mdp files? :) 1. use pdb2gmx on an unsolvated .gro to get your protein .top 2. use editconf to set the simulation box how you want it 3. use genbox -p to add solvent and take care of modifying your .top (unless your solvent is not water, in which case you'll probably have to do some manual editing of your .top) 4. grompp and mdrun Perhaps doing some tutorial material will make this and other workflows more readily understood? 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/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] top file
Helllo, I got top file using pdb2gmx but I did not comment unnecessary lines at the end of the file ( no water in my system ). With this top file I energy minimized my system. I wanted to know if I am fine ...? Thank you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to determine the box size
jojo J wrote: Hello Mark, Thank you for your reply. AS for the steps you mentioned to solvate a molecule: I have a simple molecule replicated by genconf -nbox in one direction. When I try to energy minimize this single molecule grompp em gives error: rlist is longer than half box size or longer than shortest diagnal boz size... I increase the size and everything is fine but can you please tell me what is the criterion to specify the size. Does boxsize affect results in MD? ( I am asking this because if I want to use genconf to replicate this molecule which is in a large boxzise the final size of the system can become very large so I have to use editconf to reduce the size again) http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention ...and perhaps some textbook reading. If you make a system too small, you'll waste a whole lot of time generating meaningless trajectories. Also sometimes some parts of the molcule in the box are outside the box when I see the trajectory (ngmx) at the beginning.. and I think because of the pbc it jups inthebox from the otherside. Should the particle be entirely in box at the beginning? Depends on how you set it up. In the absence of the actual commands you used, there's no way to know whether you've positioned your molecule properly. -Justin Thanks, On 8 July 2010 01:47, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Please start new emails for new discussion topics. That way you increase the chance that people with the interest and expertise can use their time efficiently, and that you get an answer. Also, archives work better if you separate topics. Please Let me ask two more simple questions about solvating a molecule. I am using genbox to solvate a solute. I have solute.gro and solvent.gro. What should be the dimension of box in solvent.gro if i want to put -nmol numbers in the solute box. Does it matter what size the box of solvent is (last line in gro)? I don't think you are using the right tool for your problem, but your description is so opaque it's hard to tell. genbox -nmol will try to fill interstices, which need to exist for it to do any good. That means you need to have prepared your solvent.gro with your solute in mind. I have solvated the solute with 50 moleecules of solvent. I have the structure file obtained from genbox. To run em or MD I need to have top file. so I am using pdb2gmx and I get a top file for the solute and 50 solvents but I have one moleculetype (named protein by default). I am confused If I need to have 2 molecuels types for solute and solvent, also if I need to enter the number of solvent molecules at the end of the top file [mols] option, or what I have now is fine and I can proceed to em and md usuing mdp files? :) 1. use pdb2gmx on an unsolvated .gro to get your protein .top 2. use editconf to set the simulation box how you want it 3. use genbox -p to add solvent and take care of modifying your .top (unless your solvent is not water, in which case you'll probably have to do some manual editing of your .top) 4. grompp and mdrun Perhaps doing some tutorial material will make this and other workflows more readily understood? Mark -- 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/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/mailing_lists/users.php -- 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/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/mailing_lists/users.php
Re: [gmx-users] top file
jojo J wrote: Helllo, I got top file using pdb2gmx but I did not comment unnecessary lines at the end of the file ( no water in my system ). With this top file I energy minimized my system. I wanted to know if I am fine ...? Depends on your definition of fine. Do you mean to ask if you've done the procedure right, or if the results should be trusted, or something else? -Justin Thank you, -- 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/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/mailing_lists/users.php
Re: [gmx-users] top file
Hello, Thank you for your answer. I mean if I need to go back and comment those lines. (if the results are trusted ..actually I forgot to comment the lines..) On 8 July 2010 23:10, Justin A. Lemkul jalem...@vt.edu wrote: jojo J wrote: Helllo, I got top file using pdb2gmx but I did not comment unnecessary lines at the end of the file ( no water in my system ). With this top file I energy minimized my system. I wanted to know if I am fine ...? Depends on your definition of fine. Do you mean to ask if you've done the procedure right, or if the results should be trusted, or something else? -Justin Thank you, -- 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/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] top file
jojo J wrote: Hello, Thank you for your answer. I mean if I need to go back and comment those lines. (if the results are trusted ..actually I forgot to comment the lines..) There's no need to comment out lines referring to solvent, ions, etc if they are not present. These statements just include extra (unnecessary) information. For more, see Chapter 5 of the Gromacs manual, and the short version of the topic here to understand what's going on: http://www.gromacs.org/Documentation/Include_File_Mechanism -Justin On 8 July 2010 23:10, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: jojo J wrote: Helllo, I got top file using pdb2gmx but I did not comment unnecessary lines at the end of the file ( no water in my system ). With this top file I energy minimized my system. I wanted to know if I am fine ...? Depends on your definition of fine. Do you mean to ask if you've done the procedure right, or if the results should be trusted, or something else? -Justin Thank you, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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/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/mailing_lists/users.php -- 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/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/mailing_lists/users.php
Re: [gmx-users] how to determine the box size
On 9/07/2010 12:59 PM, jojo J wrote: Hello Mark, Thank you for your reply. AS for the steps you mentioned to solvate a molecule: I have a simple molecule replicated by genconf -nbox in one direction. When I try to energy minimize this single molecule grompp em gives error: rlist is longer than half box size or longer than shortest diagnal boz size... I increase the size and everything is fine but can you please tell me what is the criterion to specify the size. Does boxsize affect results in MD? ( I am asking this because if I want to use genconf to replicate this molecule which is in a large boxzise the final size of the system can become very large so I have to use editconf to reduce the size again) Your conception of the workflow seems a bit confused. If you want to minimize your initial configuration before replication, then it is best to do that with an .mdp file that turns off PBC. Some reading in section 7.3 of the manual will (eventually) let you see how to do that - and what you don't need to know right now will be useful later. Alternatively, make the box size large enough now, do EM. Then, with the post-minimization structure, pick a box size suitable for replication, then use genconf. Then, do whatever you want to do with the replicated structure. Mark Also sometimes some parts of the molcule in the box are outside the box when I see the trajectory (ngmx) at the beginning.. and I think because of the pbc it jups inthebox from the otherside. Should the particle be entirely in box at the beginning? Thanks, On 8 July 2010 01:47, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Please start new emails for new discussion topics. That way you increase the chance that people with the interest and expertise can use their time efficiently, and that you get an answer. Also, archives work better if you separate topics. Please Let me ask two more simple questions about solvating a molecule. I am using genbox to solvate a solute. I have solute.gro and solvent.gro. What should be the dimension of box in solvent.gro if i want to put -nmol numbers in the solute box. Does it matter what size the box of solvent is (last line in gro)? I don't think you are using the right tool for your problem, but your description is so opaque it's hard to tell. genbox -nmol will try to fill interstices, which need to exist for it to do any good. That means you need to have prepared your solvent.gro with your solute in mind. I have solvated the solute with 50 moleecules of solvent. I have the structure file obtained from genbox. To run em or MD I need to have top file. so I am using pdb2gmx and I get a top file for the solute and 50 solvents but I have one moleculetype (named protein by default). I am confused If I need to have 2 molecuels types for solute and solvent, also if I need to enter the number of solvent molecules at the end of the top file [mols] option, or what I have now is fine and I can proceed to em and md usuing mdp files? :) 1. use pdb2gmx on an unsolvated .gro to get your protein .top 2. use editconf to set the simulation box how you want it 3. use genbox -p to add solvent and take care of modifying your .top (unless your solvent is not water, in which case you'll probably have to do some manual editing of your .top) 4. grompp and mdrun Perhaps doing some tutorial material will make this and other workflows more readily understood? 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/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energygrp_excl and PME
Hi everyone; I am simulating a functionalized nanotube with (CH3) group .the nanotube atoms are uncharged and rigid but the atoms of (CH3) group are charged and flexible ,and are defined in the residue name of [atom] section of topology file with (CNT)and (FUNC) , Respectively. I have decided to freeze my CNT in all 3 directions. In fact , I have flexible group anchored to a frozen surface of CNT . thus , I used (energygrp_exl = CNT CNT , freezegrps = CNT , coulombtype = PME ) ,but I get the following warning upon running grompp. Can not exclude the lattice coulomb energy between energy groups Please correct my .mdp file and add any requisite option in this p case. coulombtype= PME energygrps= CNT FUNC constraints = none energygrp_excl = CNT CNT freezegrps = CNT freezedim= Y Y Y Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Adding ions
Hi, When I start from a energy minimized protein in vacuum and solvate it using genbox, the output message says that the protein has zero charge. So I skip the genion step. I follow this with energy minimization of the solvated protein followed by restraining the protein and then doing a short mdrun (as is the usual procedure outlined in most tutorials). However, when I run the grompp command as the first step for the position restrained md, it runs but prints a note saying that the system has non-zero charge ~ - 0.. NOTE 2 [file finalnoss.top, line 8070]: System has non-zero total charge: -9.94e-01 I dont understand. Do I need to run the genion step anyway or is it okay to continue with this system? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
