Re: [gmx-users] Time unit issue with g_anaeig
On 14/11/2011 5:46 PM, Kei Sit wrote: Hi all, I'm new to gromacs so I hope I haven't done something wrong that is extremely simple. I have recently been using gromacs to analyse an MD trajectory using g_covar and g_anaeig. I have output saved to the trajectory every ps and I currently have a trajectory with 49000 frames (49ns). I initiate g_anaeig with this command: g_anaeig --v eigenvec.trr --f 1-21.trr --s protein.pdb --eig eigenval.xvg --proj projection.xvg --xvgr --first 1 --last 8 While this is being executed I see this: Reading frame 1000 time 100.00 which continues increasing as more frames are read. When I go to visualise projection.xvg, the time scale is in ps (natural as the default value is in ps) but it only shows 4900ps and not 49000ps. My issue is this, why is the time constantly 10 times smaller than the number of frames that are being read? Am I not entering something correctly which fixes this? What does gmxcheck have to say about your trajectory files? 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] orca and Segmentation fault
dear sir : I installed gromacs-orca for qm/mm ./configure --without-qmmm-orca --with--qmmm-gaussian --enable-mpi make make install MPI is lam-mpi when run mdrun , the error Back Off! I just backed up md.log to ./#md.log.12# Getting Loaded... Reading file pyp.tpr, VERSION 4.5.1 (single precision) Loaded with Money QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. there we go! there we go! there we go! there we go! there we go! there we go! there we go! Layer 0 nr of QM atoms 22 QMlevel: B3LYP/3-21G orca initialised... [localhost:17937] *** Process received signal *** [localhost:17939] *** Process received signal *** [localhost:17937] Signal: Segmentation fault (11) [localhost:17937] Signal code: Address not mapped (1) [localhost:17937] Failing at address: 0x10 [localhost:17940] *** Process received signal *** [localhost:17939] Signal: Segmentation fault (11) [localhost:17939] Signal code: Address not mapped (1) [localhost:17939] Failing at address: 0x10 [localhost:17936] *** Process received signal *** [localhost:17936] Signal: Segmentation fault (11) [localhost:17936] Signal code: Address not mapped (1) [localhost:17936] Failing at address: 0x10 [localhost:17934] *** Process received signal *** [localhost:17938] *** Process received signal *** [localhost:17934] Signal: Segmentation fault (11) [localhost:17934] Signal code: Address not mapped (1) [localhost:17934] Failing at address: 0x10 [localhost:17940] Signal: Segmentation fault (11) [localhost:17940] Signal code: Address not mapped (1) [localhost:17940] Failing at address: 0x10 [localhost:17938] Signal: Segmentation fault (11) [localhost:17938] Signal code: Address not mapped (1) [localhost:17938] Failing at address: 0x10 [localhost:17939] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17939] [ 1] mdrun_dd [0x534a93] [localhost:17939] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17939] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17939] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17939] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17939] [ 6] mdrun_dd [0x41bcfa] [localhost:17939] *** End of error message *** [localhost:17936] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17936] [ 1] mdrun_dd [0x534a93] [localhost:17936] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17936] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17936] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17936] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17936] [ 6] mdrun_dd [0x41bcfa] [localhost:17936] *** End of error message *** [localhost:17940] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17940] [ 1] mdrun_dd [0x534a93] [localhost:17940] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17940] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17940] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17940] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17940] [ 6] mdrun_dd [0x41bcfa] [localhost:17940] *** End of error message *** there we go! [localhost:17935] *** Process received signal *** [localhost:17935] Signal: Segmentation fault (11) [localhost:17935] Signal code: Address not mapped (1) [localhost:17935] Failing at address: 0x10 [localhost:17935] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17935] [ 1] mdrun_dd [0x534a93] [localhost:17935] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17935] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17935] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17935] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17935] [ 6] mdrun_dd [0x41bcfa] [localhost:17935] *** End of error message *** [localhost:17934] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17934] [ 1] mdrun_dd [0x534a93] [localhost:17934] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17934] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17934] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17934] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17934] [ 6] mdrun_dd [0x41bcfa] [localhost:17934] *** End of error message *** [localhost:17937] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17937] [ 1] mdrun_dd [0x534a93] [localhost:17937] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17937] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17937] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17937] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17937] [ 6] mdrun_dd [0x41bcfa] [localhost:17937] *** End of error message *** [localhost:17938] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17938] [ 1] mdrun_dd [0x534a93] [localhost:17938] [ 2]
[gmx-users] Problem about simulation at high temperature and ratio of sencondary stuctures
Hi Gromacs users, I am using GROMACS (ver4.5.3) to run molecular dynamics (MD) simulation. However during my simulation runs, I encountered some problems as stated below: 1. In NPT condition, the box size undergoes changes, especially at high temperature simulations. However, during semisotropic pressure coupling, the box size changed dramatically at x/y or z direction. That made the box thin and long or flat. On the top of that, it caused fatal error in the runs and the simulations stopped running altogether. Can this situation be prevented ? If so, how can it be done? 2. I have found that command “g_helix” can calculate helix properties. Nevertheless, my concern is with beta sheet. I did not find any tools in Gromacs that can calculate the ratio of beta sheet from MD trajectories. Do you have any recommendations? I'd appreciate any help you can give me on this and am looking forward to hearing from you soon. -- 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] Atomtype 'CR' not found
Hiii All... I want to do steepest descent energy minimization for molecule Bromobenzisoxazolone Barretin, I have all the required files like.itp and .gro. Also, changed force field from ffG43a1 to ffgmx but no use. Same error of Atomtype 'CR' not found, is coming again n again. Please suggest me possible corrections. Thanks in advance Radhika -- 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] orca and Segmentation fault
Dear xi zhao, In your case GMX is applying threading and thus not only a single QM job is requested, but eight. You should run mdrun with -nt 1. Then GMX uses only one single CPU and ORCA is called only once (but can be used in parallel). Hope that helps, Christoph On 11/14/2011 10:34 AM, xi zhao wrote: dear sir : I installed gromacs-orca for qm/mm ./configure --without-qmmm-orca --with--qmmm-gaussian --enable-mpi make make install MPI is lam-mpi when run mdrun , the error Back Off! I just backed up md.log to ./#md.log.12# Getting Loaded... Reading file pyp.tpr, VERSION 4.5.1 (single precision) Loaded with Money QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. there we go! there we go! there we go! there we go! there we go! there we go! there we go! Layer 0 nr of QM atoms 22 QMlevel: B3LYP/3-21G orca initialised... [localhost:17937] *** Process received signal *** [localhost:17939] *** Process received signal *** [localhost:17937] Signal: Segmentation fault (11) [localhost:17937] Signal code: Address not mapped (1) [localhost:17937] Failing at address: 0x10 [localhost:17940] *** Process received signal *** [localhost:17939] Signal: Segmentation fault (11) [localhost:17939] Signal code: Address not mapped (1) [localhost:17939] Failing at address: 0x10 [localhost:17936] *** Process received signal *** [localhost:17936] Signal: Segmentation fault (11) [localhost:17936] Signal code: Address not mapped (1) [localhost:17936] Failing at address: 0x10 [localhost:17934] *** Process received signal *** [localhost:17938] *** Process received signal *** [localhost:17934] Signal: Segmentation fault (11) [localhost:17934] Signal code: Address not mapped (1) [localhost:17934] Failing at address: 0x10 [localhost:17940] Signal: Segmentation fault (11) [localhost:17940] Signal code: Address not mapped (1) [localhost:17940] Failing at address: 0x10 [localhost:17938] Signal: Segmentation fault (11) [localhost:17938] Signal code: Address not mapped (1) [localhost:17938] Failing at address: 0x10 [localhost:17939] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17939] [ 1] mdrun_dd [0x534a93] [localhost:17939] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17939] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17939] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17939] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17939] [ 6] mdrun_dd [0x41bcfa] [localhost:17939] *** End of error message *** [localhost:17936] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17936] [ 1] mdrun_dd [0x534a93] [localhost:17936] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17936] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17936] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17936] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17936] [ 6] mdrun_dd [0x41bcfa] [localhost:17936] *** End of error message *** [localhost:17940] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17940] [ 1] mdrun_dd [0x534a93] [localhost:17940] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17940] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17940] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17940] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17940] [ 6] mdrun_dd [0x41bcfa] [localhost:17940] *** End of error message *** there we go! [localhost:17935] *** Process received signal *** [localhost:17935] Signal: Segmentation fault (11) [localhost:17935] Signal code: Address not mapped (1) [localhost:17935] Failing at address: 0x10 [localhost:17935] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17935] [ 1] mdrun_dd [0x534a93] [localhost:17935] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17935] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17935] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17935] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17935] [ 6] mdrun_dd [0x41bcfa] [localhost:17935] *** End of error message *** [localhost:17934] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17934] [ 1] mdrun_dd [0x534a93] [localhost:17934] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17934] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17934] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17934] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17934] [ 6] mdrun_dd [0x41bcfa] [localhost:17934] *** End of error message *** [localhost:17937] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17937] [ 1] mdrun_dd [0x534a93] [localhost:17937] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17937] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17937] [ 4] mdrun_dd(main+0xe69)
[gmx-users] Could g_order be used to calculate the order parameters for the two bonds C1'-H1', C3'-H3' in DNA?
Dear all, Recently, I have performed simulation on a B-DNA using gromacs, and I want to use g_order in gromacs to get the order parameters for the bonds C1'-H1', C3'-H3'. Is it possible to obtain order parameters for these two bonds with g_order? If possible, Would you please tell me the correct way to get order parameters for C1'-H1', C3'-H3'? Thank you very much! jnsong P.S. I just had a try using g_order, the process is as follows: - a C1' Found 24 atoms with name C1' 11 C1' :24 atoms a H1' Found 24 atoms with name H1' 12 H1' :24 atoms del 0-10 Removed group 0 'System' Removed group 1 'DNA' Removed group 2 'K' Removed group 3 'CL' Removed group 4 'Water' Removed group 5 'SOL' Removed group 6 'non-Water' Removed group 7 'Ion' Removed group 8 'K' Removed group 9 'CL' Removed group 10 'Water_and_ions' q - through this I get index.ndx for C1'-H1' and then I perform: g_order -f md.xtc -s md.tpr -n index.ndx -o and I get order.xvg, but there are no order parameters in order.xvg and the contents of order.xvg are as follows: -- # This file was created Thu Nov 10 20:00:06 2011 # by the following command: # g_order -f md.xtc -n index.ndx -s md.tpr -o -ob # # g_order is part of G R O M A C S: # # GROup of MAchos and Cynical Suckers # @title Order tensor diagonal elements @xaxis label Atom @yaxis label S @TYPE xy -- -- 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] orca and Segmentation fault
./configure --without-qmmm-orca --without--qmmm-gaussian --enable-mpi make make install I installed gromacs with Parallel mode, is not threading. when I run mpirun -np 1 mdrun_dd -v -s pyp.tpr or mdrun_dd -nt 1 -v -s pyp.tpr it still Back Off! I just backed up md.log to ./#md.log.20# Getting Loaded... Reading file pyp.tpr, VERSION 4.5.1 (single precision) Loaded with Money QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 22 QMlevel: B3LYP/3-21G orca initialised... Back Off! I just backed up traj.trr to ./#traj.trr.1# Back Off! I just backed up traj.xtc to ./#traj.xtc.1# Back Off! I just backed up ener.edr to ./#ener.edr.2# starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water' 500 steps, 0.5 ps. Calling 'orca pyp.inp pyp.out' Error : multiplicity (Mult:=2*S+1) is zero --- Program mdrun_dd, VERSION 4.5.1 Source code file: qm_orca.c, line: 393 Fatal error: Call to 'orca pyp.inp pyp.out' failed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The Carpenter Goes Bang Bang (The Breeders) Halting program mdrun_dd gcq#129: The Carpenter Goes Bang Bang (The Breeders) -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- -- mpirun has exited due to process rank 0 with PID 18080 on node localhost.localdomai exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). --- 11年11月14日，周一, Christoph Riplinger c...@thch.uni-bonn.de 写道： 发件人: Christoph Riplinger c...@thch.uni-bonn.de 主题: Re: [gmx-users] orca and Segmentation fault 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2011年11月14日,周一,下午6:51 Dear xi zhao, In your case GMX is applying threading and thus not only a single QM job is requested, but eight. You should run mdrun with -nt 1. Then GMX uses only one single CPU and ORCA is called only once (but can be used in parallel). Hope that helps, Christoph On 11/14/2011 10:34 AM, xi zhao wrote: dear sir : I installed gromacs-orca for qm/mm ./configure --without-qmmm-orca --without--qmmm-gaussian --enable-mpi make make install MPI is lam-mpi when run mdrun , the error Back Off! I just backed up md.log to ./#md.log.12# Getting Loaded... Reading file pyp.tpr, VERSION 4.5.1 (single precision) Loaded with Money QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. QM/MM calculation requested. there we go! there we go! there we go! there we go! there we go! there we go! there we go! Layer 0 nr of QM atoms 22 QMlevel: B3LYP/3-21G orca initialised... [localhost:17937] *** Process received signal *** [localhost:17939] *** Process received signal *** [localhost:17937] Signal: Segmentation fault (11) [localhost:17937] Signal code: Address not mapped (1) [localhost:17937] Failing at address: 0x10 [localhost:17940] *** Process received signal *** [localhost:17939] Signal: Segmentation fault (11) [localhost:17939] Signal code: Address not mapped (1) [localhost:17939] Failing at address: 0x10 [localhost:17936] *** Process received signal *** [localhost:17936] Signal: Segmentation fault (11) [localhost:17936] Signal code: Address not mapped (1) [localhost:17936] Failing at address: 0x10 [localhost:17934] *** Process received signal *** [localhost:17938] *** Process received signal *** [localhost:17934] Signal: Segmentation fault (11) [localhost:17934] Signal code: Address not mapped (1) [localhost:17934] Failing at address: 0x10 [localhost:17940] Signal: Segmentation fault (11) [localhost:17940] Signal code: Address not mapped (1) [localhost:17940] Failing at address: 0x10 [localhost:17938] Signal: Segmentation fault (11) [localhost:17938] Signal code: Address not mapped (1) [localhost:17938] Failing at address: 0x10 [localhost:17939] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430] [localhost:17939] [ 1] mdrun_dd [0x534a93] [localhost:17939] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1] [localhost:17939] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c] [localhost:17939] [ 4] mdrun_dd(main+0xe69) [0x43d619] [localhost:17939] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x35c4f1c3fb] [localhost:17939] [ 6] mdrun_dd [0x41bcfa] [localhost:17939] *** End of error message *** [localhost:17936] [ 0] /lib64/tls/libpthread.so.0
RE: [gmx-users] Potential Energy Landscape
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 21 October 2011 13:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Potential Energy Landscape Natalie Stephenson wrote: Hi Justin (and gmx-users), I've been looking into using g_sham for the free energy landscapes, however I'm not sure what variables I should plot ... could I just use the g_energy (potential) outputs to produce the energy landscape?? Other examples I've seen using g_sham have done quite in depth eigenvector projections before plotting them using g_sham. The free energy of potential energy is probably not a meaningful quantity ;) What inputs would I require in order to determine how loading rate an increased loading rate on the simulation would change the force results? I know I'm probably being completely dumb but my use of maths has been sporadic to say the least in the last 7 years ... so getting back into it is proving more confusing! You haven't provided a lot of detail about what you're doing, what you've measured, or what you hope to achieve. In general, one plots two variables (one on each axis), and g_sham calculates a free energy based simply on the probability of occurrence of these values. For instance, for protein folding experiments, often the RMSD relative to the known structure is one variable, and something else like native contacts or hydrogen bonds is plotted as the other variable. The free energy surface is then generated as a function of intramolecular association and similarity to a known structure. -Justin Sorry it's taken so long to reply to this one, experimental issues dragged my focus! I have performed force pulling experiments on a protein with both Gromacs MD simulations and experimentally with AFM. The problem I'm facing with the data is the difference between the loading rates of the two approaches. For the MDS the loading rate is around 10 N/s, whereas the AFM experiments have a much lower loading rate of 1 x 10^-8 N/s. I was told at a conference I attended that there was a way of constructing a 'potential energy landscape' which would be able to use this to remove the loading rate differences. However, I did not get a chance to find out how this was possible. I understand how g_sham works, however, I'm not sure what - in this case - the input would be in order to construct such a 'potential energy landscape'. Any insight into how I would be able to create this ... or any other ideas on how I would be able to somehow relate the simulation output to experimental data dispite the loading rate differences would be GREATLY appreciated!! Thanks once again!! Natalie Natalie Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 12 October 2011 18:22 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Potential Energy Landscape Natalie Stephenson wrote: I was recently told in passing that it would be possible to construct a 'potential energy landscape' from the simulations I have performed. This way I could remove any loading rate differences between simulations and experimental force experiments I've been performing ... however I cannot find anywhere in which this is mentioned. The only thing close I could find that was close was the free energy landscape using g_anaeig under the Dihedral PCA (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca) however, I'm not sure this is what I'm looking for. Does anyone know where I would be able to find out / read more about how to create potential energy landscapes from my simulation outputs? g_sham produces free energy landscapes for any variables plotted against one another. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --
Re: [gmx-users] Atomtype 'CR' not found
On 14/11/2011 9:08 PM, radhika jaswal wrote: Hiii All... I want to do steepest descent energy minimization for molecule Bromobenzisoxazolone Barretin, I have all the required files like.itp and .gro. Also, changed force field from ffG43a1 to ffgmx but no use. Same error of Atomtype 'CR' not found, is coming again n again. Please suggest me possible corrections. Having the files is just not enough - they've got to have contents that make sense in the context of the force field. You need to find a force field whose atom types include suitable models for this compound. The .itp needs to be generated for the force field. So wherever you sourced these files determines the force field. 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: orca and Segmentation fault (xi zhao)
THe error message is clear: your spin multiplicity is 0, which is impossible. Please make sure you understand the basics of electronic structure theory. To test this, you can run the QM system only in stand along QM package. gerrit 2. Re: orca and Segmentation fault (xi zhao) 3. RE: Potential Energy Landscape (Natalie Stephenson) - ./configure --without-qmmm-orca --without--qmmm-gaussian --enable-mpi make make install I installed gromacs with Parallel  mode, is not threading. when I run  mpirun -np 1 mdrun_dd -v -s pyp.tpr or mdrun_dd -nt 1 -v -s pyp.tpr it still Back Off! I just backed up md.log to ./#md.log.20# Getting Loaded... Reading file pyp.tpr, VERSION 4.5.1 (single precision) Loaded with Money QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 22 QMlevel: B3LYP/3-21G orca initialised... Back Off! I just backed up traj.trr to ./#traj.trr.1# Back Off! I just backed up traj.xtc to ./#traj.xtc.1# Back Off! I just backed up ener.edr to ./#ener.edr.2# starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water' 500 steps,     0.5 ps. Calling 'orca pyp.inp pyp.out' Error : multiplicity (Mult:=2*S+1) is zero --- Program mdrun_dd, VERSION 4.5.1 Source code file: qm_orca.c, line: 393 Fatal error: Call to 'orca pyp.inp pyp.out' failed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The Carpenter Goes Bang Bang (The Breeders) Halting program mdrun_dd gcq#129: The Carpenter Goes Bang Bang (The Breeders) -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- -- mpirun has exited due to process rank 0 with PID 18080 on node localhost.localdomai exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). --- 11年11月14日，周一, Christoph Riplingerc...@thch.uni-bonn.de 写�： �件人: Christoph Riplingerc...@thch.uni-bonn.de 主题: Re: [gmx-users] orca and Segmentation fault 收件人: Discussion list for GROMACS usersgmx-users@gromacs.org 日期: 2011年11月14日,周一,下�6:51 -- 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] Problem about simulation at high temperature and ratio of sencondary stuctures
On 14/11/2011 8:33 PM, ??? wrote: Hi Gromacs users, I am using GROMACS (ver4.5.3) to run molecular dynamics (MD) simulation. However during my simulation runs, I encountered some problems as stated below: 1. In NPT condition, the box size undergoes changes, especially at high temperature simulations. However, during semisotropic pressure coupling, the box size changed dramatically at x/y or z direction. That made the box thin and long or flat. On the top of that, it caused fatal error in the runs and the simulations stopped running altogether. Can this situation be prevented ? If so, how can it be done? Perhaps the models in your systems are intrinsically unsuited to these simulation conditions. To my knowledge, no common biomolecular force field has been parametrized against high-temperature NPT data. Under these conditions, the assumptions about safe sizes for integration time steps need not hold, so you may find smaller steps are more stable. 2. I have found that command g_helix can calculate helix properties. Nevertheless, my concern is with beta sheet. I did not find any tools in Gromacs that can calculate the ratio of beta sheet from MD trajectories. Do you have any recommendations? do_dssp with old-style DSSP installed is the only GROMACS offering that can address this. Check out manual section 7.4 for overviews of tools. 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] mpirun with remd
dear teacher, when i do remd ,i use the commond : mpirun n8,8,8,8,9,10,15,16,16,20,20,22 -np 24 /export/software/bin/mdrun_mpi_4.5.5 -multidir ./0/ ./1/ ./2/ ./3/ ./4/ ./5/ ./6/ ./7/ ./8/ ./9/ ./10/ ./11/ -replex 1000 -nice 0 -s pmma.tpr -o md -c after_md -pd -table table.xvg -tableb table.xvg -v log1 node16: PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 14411 KD16 0 51528 3552 2728 R 67.6 0.1 6:47.63 mdrun_mpi_4.5.5 14409 KD15 0 51528 3612 2788 S 25.9 0.1 1:22.06 mdrun_mpi_4.5.5 14408 KD15 0 51516 3396 2580 S 22.2 0.1 1:10.81 mdrun_mpi_4.5.5 14410 KD15 0 51508 3212 2408 S 20.6 0.1 1:07.22 mdrun_mpi_4.5.5 and we have 4 cpus on this node16 there are no other program except the system's:, why only one %CPU of thread (14411 ) is big ? thanks! regards, Bo Du Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 E-mail: 2008d...@gmail.com -- 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] mpirun with remd
On 15/11/2011 12:22 AM, 杜波 wrote: dear teacher, when i do remd ,i use the commond : mpirun n8,8,8,8,9,10,15,16,16,20,20,22 -np 24 /export/software/bin/mdrun_mpi_4.5.5 -multidir ./0/ ./1/ ./2/ ./3/ ./4/ ./5/ ./6/ ./7/ ./8/ ./9/ ./10/ ./11/ -replex 1000 -nice 0 -s pmma.tpr -o md -c after_md -pd -table table.xvg -tableb table.xvg -v log1 node16: PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 14411 KD 16 0 51528 3552 2728 R 67.6 0.1 6:47.63 mdrun_mpi_4.5.5 14409 KD 15 0 51528 3612 2788 S 25.9 0.1 1:22.06 mdrun_mpi_4.5.5 14408 KD 15 0 51516 3396 2580 S 22.2 0.1 1:10.81 mdrun_mpi_4.5.5 14410 KD 15 0 51508 3212 2408 S 20.6 0.1 1:07.22 mdrun_mpi_4.5.5 and we have 4 cpus on this node16 there are no other program except the system's:, why only one %CPU of thread (14411 ) is big ? We don't really know enough to say. We don't know that this percentage is a valid metric on your system or that your mpirun invocation is valid. Set up a run that should take a few minutes and compare the time taken in serial with one or two processors, and with REMD systems of various numbers of replicas. Now you can start to track down what, if any, problem is occurring. 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] GROMACS/ORCA QMMM
Dear Jose, I tried oniom which stopped for me either (although without a segfault). Have you tried QMMMscheme normal? Christoph On 11/11/2011 05:53 PM, Jose Tusell wrote: Dear GROMACS users, I'm trying to run a QM-MM optimization. I solvate my protein and add ions then I do a classical optimization (just GROMACS). After that I run grompp with the following minim.mdp file (just showing qmmm options): QMMM= yes QMMM-grps = Other QMmethod= RHF QMbasis = 3-21G QMMMscheme = Oniom QMcharge= -1 QMmult = 1 SH = no This creates the *.tpr file that use to run mdrun. I use the following *.ORCAINFO file: !PAL8 Quick-DFT VerySlowConv %scf Maxiter 300 end %pal nprocs 8 end The ORCA run quickly converges but after that mdrun run stops with a segmentation fault. Am I missing something in all of this? Any help would be greatly appreciated. Thanks Jose Tusell -- 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] The equilibrium before REMD simulations
Dear GMX users, I am puzzled about some technical details regarding to the REMD simulation and eager for your generous help. With the purpose to explore the additional conformational space of the protein, I want to employ the REMD method in Gromacs. However, I noticed that in almost all of the papers about REMD, a short equilibrium with NPT or NVT was performed for each replica respectively before the final REMD run. But i think the initial structure of each replica for REMD run is thus different due to the respective equilibrium and may somewhat go against the concept of replicas which i suppose should have same initial structures while with different temperatures. So my question is whether we should or not perform the NVT or NPT equilibrium before REMD simulations BTW and why? BTW, i also want to know which ensemble should we use in REMD because some papers use NPT while others use NVT. Thanks in advance! Best regards! Xiangqian Kong -- 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] The equilibrium before REMD simulations
ÏéÇ« ¿× wrote: Dear GMX users, I am puzzled about some technical details regarding to the REMD simulation and eager for your generous help. With the purpose to explore the additional conformational space of the protein, I want to employ the REMD method in Gromacs. However, I noticed that in almost all of the papers about REMD, a short equilibrium with NPT or NVT was performed for each replica respectively before the final REMD run. But i think the initial structure of each replica for REMD run is thus different due to the respective equilibrium and may somewhat go against the concept of replicas which i suppose should have same initial structures while with different temperatures. So my question is whether we should or not perform the NVT or NPT equilibrium before REMD simulations BTW and why? BTW, i also want to know which ensemble Yes, always equilibrate. Otherwise, your systems will almost certainly not be stable. Position restraints are typically applied to the solute of interest during the initial equilibration, making initial differences almost insignificant. should we use in REMD because some papers use NPT while others use NVT. Pressure coupling algorithms frequently break down at high temperature, so NVT is often used. -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] Units of Buckingham potential
Hi dear all, For Buckingham potential， there is three parameters A B C In GMX, the units of A B C is the kJ/mol, nm, kJ/mol*nm^6， am I right? Best XJ -- 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] Units of Buckingham potential
On 15/11/2011 2:00 AM, xiaojing gong wrote: Hi dear all, For Buckingham potential， there is three parameters A B C In GMX, the units of A B C is the kJ/mol, nm, kJ/mol*nm^6， am I right? Manual section 2.2 defines the units, and 4.1.2 defines the functional form. 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] The equilibrium before REMD simulations
Dear Justin, Thanks for your prompt reply! As you say, we should equilibrium each replica at its initial target temperature. So i guess we may do the followings: First, after the minimization and heating, we use NPT to equilibrium the density of the system. And then with the same initial system,equilibrium every replica at their target temperature with NVT ensemble to avoid the instability during REMD and keep the volume constant among the replicas. Finally, do the REMD simulations. Is this workflow reasonable enough and do you have any better guide? Any suggestions will be greatly appreciated! Best regards! Xiangqian Kong --- On Mon, 11/14/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] The equilibrium before REMD simulations To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, November 14, 2011, 10:25 PM ÏéÇ« ¿× wrote: Dear GMX users, I am puzzled about some technical details regarding to the REMD simulation and eager for your generous help. With the purpose to explore the additional conformational space of the protein, I want to employ the REMD method in Gromacs. However, I noticed that in almost all of the papers about REMD, a short equilibrium with NPT or NVT was performed for each replica respectively before the final REMD run. But i think the initial structure of each replica for REMD run is thus different due to the respective equilibrium and may somewhat go against the concept of replicas which i suppose should have same initial structures while with different temperatures. So my question is whether we should or not perform the NVT or NPT equilibrium before REMD simulations BTW and why? BTW, i also want to know which ensemble Yes, always equilibrate. Otherwise, your systems will almost certainly not be stable. Position restraints are typically applied to the solute of interest during the initial equilibration, making initial differences almost insignificant. should we use in REMD because some papers use NPT while others use NVT. Pressure coupling algorithms frequently break down at high temperature, so NVT is often used. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] The equilibrium before REMD simulations
ÏéÇ« ¿× wrote: Dear Justin, Thanks for your prompt reply! As you say, we should equilibrium each replica at its initial target temperature. So i guess we may do the followings: First, after the minimization and heating, we use NPT to equilibrium the density of the system. And then with the same initial system,equilibrium every replica at their target temperature with NVT ensemble to avoid the instability during REMD and keep the volume constant among the replicas. Finally, do the REMD simulations. Is this workflow reasonable enough and do you have any better guide? Any suggestions will be greatly appreciated! Seems reasonable, but I am no REMD expert. There is certainly ample literature for you to read to find a suitable established protocol, or to validate your procedure. -Justin Best regards! Xiangqian Kong --- On Mon, 11/14/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] The equilibrium before REMD simulations To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, November 14, 2011, 10:25 PM ÏéÇ« ¿× wrote: Dear GMX users, I am puzzled about some technical details regarding to the REMD simulation and eager for your generous help. With the purpose to explore the additional conformational space of the protein, I want to employ the REMD method in Gromacs. However, I noticed that in almost all of the papers about REMD, a short equilibrium with NPT or NVT was performed for each replica respectively before the final REMD run. But i think the initial structure of each replica for REMD run is thus different due to the respective equilibrium and may somewhat go against the concept of replicas which i suppose should have same initial structures while with different temperatures. So my question is whether we should or not perform the NVT or NPT equilibrium before REMD simulations BTW and why? BTW, i also want to know which ensemble Yes, always equilibrate. Otherwise, your systems will almost certainly not be stable. Position restraints are typically applied to the solute of interest during the initial equilibration, making initial differences almost insignificant. should we use in REMD because some papers use NPT while others use NVT. Pressure coupling algorithms frequently break down at high temperature, so NVT is often used. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Units of Buckingham potential
Many thanks for reply. Another question, If I use Buckingham potential for CNT, and I want to simulate CNT and water, shall I also transfer the SPC.itp from LJ to Buckingham potential? Best XJ 2011/11/14 Mark Abraham mark.abra...@anu.edu.au On 15/11/2011 2:00 AM, xiaojing gong wrote: Hi dear all, For Buckingham potential， there is three parameters A B C In GMX, the units of A B C is the kJ/mol, nm, kJ/mol*nm^6， am I right? Manual section 2.2 defines the units, and 4.1.2 defines the functional form. Mark -- 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 http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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
Re: [gmx-users] The equilibrium before REMD simulations
On 15/11/2011 2:50 AM, ÏéÇ« ¿× wrote: Dear Justin, Thanks for your prompt reply! As you say, we should equilibrium each replica at its initial target temperature. So i guess we may do the followings: First, after the minimization and heating, we use NPT to equilibrium the density of the system. And then with the same initial system,equilibrium every replica at their target temperature with NVT ensemble to avoid the instability during REMD and keep the volume constant among the replicas. Finally, do the REMD simulations. Is this workflow reasonable enough and do you have any better guide? Any suggestions will be greatly appreciated! That is a standard REMD workflow. Do check out some literature for REMD simulations similar to your system. 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] No locks available.
Hi, On Mon, Nov 14, 2011 at 2:15 AM, lina lina.lastn...@gmail.com wrote: On Mon, Nov 14, 2011 at 7:47 AM, Roland Schulz rol...@utk.edu wrote: Hi, what file system is this? What operating system on the compute node? In case it is a network file system what file system is used underneath and what operating system is the file server using? What version of GROMACS are you using? As you workaround you should be able to run with mdrun -noappend. There is no problem running a mdrun without appending. Could you please send the information about your system? I would be interested to see why it doesn't succeed to lock. Roland Roland On Sun, Nov 13, 2011 at 10:43 AM, lina lina.lastn...@gmail.com wrote: Hi, This is the first time I met: Fatal error: Failed to lock: md.log. No locks available the disk is not saturated, md.log is normal, The job was stopped months ago, and now I planned to resume it with all the necessary files kept intact. Thanks for pointing out which parts I should examine, Best regards, -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] the force constant in constant speed umbrella pulling
Hi everyone, I am just wondering about the mathematical and physical meaning of this force constant when pulling a ligand from its receptor. So I can imagine a dummy atom is linked to the ligand via a spring, and it is moving away from the receptor at 1 nm/ns with the spring force constant 1000 kJ/mol/nm^2. After it moved a very small distance, for example 0.0001 nm, which would be the change in the length of the spring, there will be a corresponding force 0.1 kJ/mol/nm, which is 0.166 pN. So is this force only directly exerted on the COM of the ligand? Or it's been distributed across every atom within the ligand? From this imagined model, is seems the force constant does not have as much effect on the quality (i.e. better quality means closer to a reversible thermodynamic process) of the pulling process as the pulling rate. But I wonder, would reducing force constant by 50% have the same effect on decreasing computational load as reducing pulling rate by 50%? Supposing a set pulled distance 5 nm is required, which one should save more computational time? Thanks for any suggestion. Yun -- 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] UNK not found in residue topology
Hello, I'm getting an UNK not found in residue topology error message. After I run pdb2gmx -f XXX.pdb -o conf.pdb Fatal error: Residue 'UNK' not found in residue topology database I figured out what the error was and tried to add UNK as carbon to ffopslaa.rtf [UNK] [ atoms ] UNK UNK 0.000 0 but I am still getting the same error. What do I do? Adrianna -- 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] GMX to remove clashes?
Hi, all, I am wondering if Gromacs can do the following work? Assuming I have a pdb file of an RNA molecule. Some atoms may be too close or even overlap, I am wondering if Gromacs can move the atoms to reasonable positions and remove the bad contacts? The final structure is supposed to be the most stable structure with minimal energy. I know AMBER minimization can do this work, and I am wondering if Gromacs can do the same? -- Best, Liang Liu -- 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] GMX to remove clashes?
Liu, Liang wrote: Hi, all, I am wondering if Gromacs can do the following work? Assuming I have a pdb file of an RNA molecule. Some atoms may be too close or even overlap, I am wondering if Gromacs can move the atoms to reasonable positions and remove the bad contacts? The final structure is supposed to be the most stable structure with minimal energy. I know AMBER minimization can do this work, and I am wondering if Gromacs can do the same? Gromacs is perfectly capable of energy minimization. Whether or not minimization succeeds and gives a reasonable output is mostly dependent upon the feasibility of the starting structure. If the minimization crashes, it's not Gromacs' fault ;) -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] UNK not found in residue topology
Janowicz, Adrianna C. wrote: Hello, I'm getting an UNK not found in residue topology error message. After I run pdb2gmx -f XXX.pdb -o conf.pdb Fatal error: Residue 'UNK' not found in residue topology database I figured out what the error was and tried to add UNK as carbon to ffopslaa.rtf There are no .rtf files used by Gromacs, so if you've created or edited one, it will have no effect. [UNK] [ atoms ] UNK UNK 0.000 0 but I am still getting the same error. What do I do? In theory, one can define a residue named UNK with atom names and types of UNK, but that's an incredibly awkward mechanism. It would probably be worthwhile to use real, existing atom types (which would be required by OPLS) with a meaningful residue name. Perhaps the format of your .pdb file is wrong and pdb2gmx is reading another column for the residue name instead of the one intended. If you specify everything as UNK, you'll never know. -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] GMX to remove clashes?
This is a reasonable answer :) Thanks for that, and I just tried Gromacs for minimization, and looks the final structure does not have clashes anymore, and also are very close to the initial structure. Another question is if there is a way to add ions automatically, meaning no need to check the NOTE of System has non-zero total charge in the output of grompp command? And also update the topology file automatically too? On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Hi, all, I am wondering if Gromacs can do the following work? Assuming I have a pdb file of an RNA molecule. Some atoms may be too close or even overlap, I am wondering if Gromacs can move the atoms to reasonable positions and remove the bad contacts? The final structure is supposed to be the most stable structure with minimal energy. I know AMBER minimization can do this work, and I am wondering if Gromacs can do the same? Gromacs is perfectly capable of energy minimization. Whether or not minimization succeeds and gives a reasonable output is mostly dependent upon the feasibility of the starting structure. If the minimization crashes, it's not Gromacs' fault ;) -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/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 http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- 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] GMX to remove clashes?
Liu, Liang wrote: This is a reasonable answer :) Thanks for that, and I just tried Gromacs for minimization, and looks the final structure does not have clashes anymore, and also are very close to the initial structure. Another question is if there is a way to add ions automatically, meaning no need to check the NOTE of System has non-zero total charge in the output of grompp command? And also update the topology file automatically too? That depends on the system. For a simple solute in water, the running total charge of the solute is recorded in the qtot column of the .top file. If you have a complex system with lots of charged things, no, there is no convenient way to get the charge aside from calculating it by hand or reading the grompp output. The topology can be modified automatically by genion after ions are added by using the -p flag. -Justin On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi, all, I am wondering if Gromacs can do the following work? Assuming I have a pdb file of an RNA molecule. Some atoms may be too close or even overlap, I am wondering if Gromacs can move the atoms to reasonable positions and remove the bad contacts? The final structure is supposed to be the most stable structure with minimal energy. I know AMBER minimization can do this work, and I am wondering if Gromacs can do the same? Gromacs is perfectly capable of energy minimization. Whether or not minimization succeeds and gives a reasonable output is mostly dependent upon the feasibility of the starting structure. If the minimization crashes, it's not Gromacs' fault ;) -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin 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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 http://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- 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] GMX to remove clashes?
Thanks. Do you know how to use a new force field, not amber or charm, but a force field built by someone else, and it's already in Gromacs format (tons of xvg file, right?) On Mon, Nov 14, 2011 at 4:13 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: This is a reasonable answer :) Thanks for that, and I just tried Gromacs for minimization, and looks the final structure does not have clashes anymore, and also are very close to the initial structure. Another question is if there is a way to add ions automatically, meaning no need to check the NOTE of System has non-zero total charge in the output of grompp command? And also update the topology file automatically too? That depends on the system. For a simple solute in water, the running total charge of the solute is recorded in the qtot column of the .top file. If you have a complex system with lots of charged things, no, there is no convenient way to get the charge aside from calculating it by hand or reading the grompp output. The topology can be modified automatically by genion after ions are added by using the -p flag. -Justin On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Liu, Liang wrote: Hi, all, I am wondering if Gromacs can do the following work? Assuming I have a pdb file of an RNA molecule. Some atoms may be too close or even overlap, I am wondering if Gromacs can move the atoms to reasonable positions and remove the bad contacts? The final structure is supposed to be the most stable structure with minimal energy. I know AMBER minimization can do this work, and I am wondering if Gromacs can do the same? Gromacs is perfectly capable of energy minimization. Whether or not minimization succeeds and gives a reasonable output is mostly dependent upon the feasibility of the starting structure. If the minimization crashes, it's not Gromacs' fault ;) -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://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-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/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 http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- 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] GMX to remove clashes?
Liu, Liang wrote: Thanks. Do you know how to use a new force field, not amber or charm, but a force field built by someone else, and it's already in Gromacs format (tons of xvg file, right?) Force fields are not in .xvg format, unless you're talking about using tabulated potentials. In either case, please see the manual and the help information on gromacs.org, and start a new thread with more information to change topics if you have further questions. -Justin On Mon, Nov 14, 2011 at 4:13 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: This is a reasonable answer :) Thanks for that, and I just tried Gromacs for minimization, and looks the final structure does not have clashes anymore, and also are very close to the initial structure. Another question is if there is a way to add ions automatically, meaning no need to check the NOTE of System has non-zero total charge in the output of grompp command? And also update the topology file automatically too? That depends on the system. For a simple solute in water, the running total charge of the solute is recorded in the qtot column of the .top file. If you have a complex system with lots of charged things, no, there is no convenient way to get the charge aside from calculating it by hand or reading the grompp output. The topology can be modified automatically by genion after ions are added by using the -p flag. -Justin On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi, all, I am wondering if Gromacs can do the following work? Assuming I have a pdb file of an RNA molecule. Some atoms may be too close or even overlap, I am wondering if Gromacs can move the atoms to reasonable positions and remove the bad contacts? The final structure is supposed to be the most stable structure with minimal energy. I know AMBER minimization can do this work, and I am wondering if Gromacs can do the same? Gromacs is perfectly capable of energy minimization. Whether or not minimization succeeds and gives a reasonable output is mostly dependent upon the feasibility of the starting structure. If the minimization crashes, it's not Gromacs' fault ;) -Justin -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-request@__gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- ==__== 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
[gmx-users] import force field
I have a serial of tabulated potentials with the name of *.xvg, which are the function of atom distance. I am wondering how to use them in gromacs simulation? Will that replace the force field, e.g. amber03? Thanks. -- Best, Liang Liu -- 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] Time unit issue with g_anaeig
Hi Mark, I ran gmxcheck and it returned the following output: Checking file 1-21.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 7764 Reading frame 49000 time 4900.000 Item#frames Timestep (ps) Step 499840.1 Time 499840.1 Lambda 499840.1 Coords 499840.1 Velocities 0 Forces 0 Box 499840.1 I understand now why the time is 10 times smaller in my analysis, but this now raises another question as to why it is 0.1ps per frame. Would it have something to do with the converting from a DCD format to a TRR format? I just checked the configuration file for my MD run and I can still see that I'm running the simulation of 2fs timesteps and saving output every 500 steps which should equate to 1ps. Once again, thank you for your time in helping. Regards, Kei From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Monday, 14 November 2011 6:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Time unit issue with g_anaeig On 14/11/2011 5:46 PM, Kei Sit wrote: Hi all, I'm new to gromacs so I hope I haven't done something wrong that is extremely simple. I have recently been using gromacs to analyse an MD trajectory using g_covar and g_anaeig. I have output saved to the trajectory every ps and I currently have a trajectory with 49000 frames (49ns). I initiate g_anaeig with this command: g_anaeig -v eigenvec.trr -f 1-21.trr -s protein.pdb -eig eigenval.xvg -proj projection.xvg -xvgr -first 1 -last 8 While this is being executed I see this: Reading frame 1000 time 100.00 which continues increasing as more frames are read. When I go to visualise projection.xvg, the time scale is in ps (natural as the default value is in ps) but it only shows 4900ps and not 49000ps. My issue is this, why is the time constantly 10 times smaller than the number of frames that are being read? Am I not entering something correctly which fixes this? What does gmxcheck have to say about your trajectory files? 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] Query on restraining center of mass of a protein
Hi, I have a system containing water and a large protein. In the simulation, I do not want the protein center of mass to drift away. I was wondering what will be the reasonable method in gromacs to fix the position of the center of mass of the protein in its original position . I was thinking about two options in gromacs. 1) use the protein as comm-grp only to remove its center of mass motion . ( or should I use both protein and non-protein ( water) center of mass as comm-grps separately ). 2) Finding the residue closest to center of mass of the protein ( but I am not sure how to do it ). Can anyone suggest which will be a good idea ? 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
RE: [gmx-users] Time unit issue with g_anaeig
Hi again, I just found the solution to the problem. Using trjconv to specify the timestep seems to have helped. Thanks again for the help. Regards, Kei From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Kei Sit Sent: Tuesday, 15 November 2011 9:20 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] Time unit issue with g_anaeig Hi Mark, I ran gmxcheck and it returned the following output: Checking file 1-21.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 7764 Reading frame 49000 time 4900.000 Item#frames Timestep (ps) Step 499840.1 Time 499840.1 Lambda 499840.1 Coords 499840.1 Velocities 0 Forces 0 Box 499840.1 I understand now why the time is 10 times smaller in my analysis, but this now raises another question as to why it is 0.1ps per frame. Would it have something to do with the converting from a DCD format to a TRR format? I just checked the configuration file for my MD run and I can still see that I'm running the simulation of 2fs timesteps and saving output every 500 steps which should equate to 1ps. Once again, thank you for your time in helping. Regards, Kei From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Monday, 14 November 2011 6:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Time unit issue with g_anaeig On 14/11/2011 5:46 PM, Kei Sit wrote: Hi all, I'm new to gromacs so I hope I haven't done something wrong that is extremely simple. I have recently been using gromacs to analyse an MD trajectory using g_covar and g_anaeig. I have output saved to the trajectory every ps and I currently have a trajectory with 49000 frames (49ns). I initiate g_anaeig with this command: g_anaeig -v eigenvec.trr -f 1-21.trr -s protein.pdb -eig eigenval.xvg -proj projection.xvg -xvgr -first 1 -last 8 While this is being executed I see this: Reading frame 1000 time 100.00 which continues increasing as more frames are read. When I go to visualise projection.xvg, the time scale is in ps (natural as the default value is in ps) but it only shows 4900ps and not 49000ps. My issue is this, why is the time constantly 10 times smaller than the number of frames that are being read? Am I not entering something correctly which fixes this? What does gmxcheck have to say about your trajectory files? 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] Query on restraining center of mass of a protein
On 15/11/2011 10:21 AM, Sanku M wrote: Hi, I have a system containing water and a large protein. In the simulation, I do not want the protein center of mass to drift away. Why do you want it not to drift away? There's nothing magical about the center of a periodic simulation cell. Why do you want to change the dynamics to achieve this? Mark I was wondering what will be the reasonable method in gromacs to fix the position of the center of mass of the protein in its original position . I was thinking about two options in gromacs. 1) use the protein as comm-grp only to remove its center of mass motion . ( or should I use both protein and non-protein ( water) center of mass as comm-grps separately ). 2) Finding the residue closest to center of mass of the protein ( but I am not sure how to do it ). Can anyone suggest which will be a good idea ? -- 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] import force field
On 15/11/2011 9:33 AM, Liu, Liang wrote: I have a serial of tabulated potentials with the name of *.xvg, which are the function of atom distance. I am wondering how to use them in gromacs simulation? Will that replace the force field, e.g. amber03? Thanks. There are sections in the manual that describe the use of tabulated potentials for either bonded or non-bonded interactions. Such tables modify the force field in the expected manner. 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] Questionable van der waals volumes from g_sas
Hello gmx-users I have been attempting to obtain van der Waal's volumes using the g_sas utility. The command I use to do so is something like g_sas -f hexane.gro -s topol.tpr -probe 0 -tv V_vdw.xvg This seems to give reasonable results for most of my test systems, however when I run the command on an optimized structure of cyclohexane I get a larger van der Waal's volume than that of n-hexane. I think this has to do with the fact that the surface calculation method used in g_sas is missing the void in the centre of the ring. In order to test this I increased the size of the ring, calculating the volumes of icosane and cycloicosane. I found that in this case the volume of the cyclic molecule was expectedly smaller. I tried increasing the number of dots used to draw the dot-surface but saw no significant change in the volumes. Therefore my question is if anybody is familiar enough with g_sas to help me understand why the surface calculation method is not giving sensible values for these smaller ring systems. Also I am wondering if anybody can suggest any other free software that would allow me to compute van der Waal's and Solvent Excluded volumes. Thanks in advance. Jake Spooner -- 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] The equilibrium before REMD simulations
Thanks for everyone's prompt reply! However, i still puzzled why we should use NVT rather than NPT in REMD simulation. As we know that isothermal-isobaric ensemble may be more relevant to the realistic experimental conditions. If the highest temperature was no more than 400K ( i think it is not very high) and the pressure coupling may still work, should NPT be a better choice? Or the NPT method would impair the physical meanings of REMD, however, some NPT examples were depicted in some papers and also in our mailing list. Best regards! Xiangqian Kong --- On Mon, 11/14/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] The equilibrium before REMD simulations To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, November 14, 2011, 11:53 PM On 15/11/2011 2:50 AM, ÏéÇ« ¿× wrote: Dear Justin, Thanks for your prompt reply! As you say, we should equilibrium each replica at its initial target temperature. So i guess we may do the followings: First, after the minimization and heating, we use NPT to equilibrium the density of the system. And then with the same initial system,equilibrium every replica at their target temperature with NVT ensemble to avoid the instability during REMD and keep the volume constant among the replicas. Finally, do the REMD simulations. Is this workflow reasonable enough and do you have any better guide? Any suggestions will be greatly appreciated! That is a standard REMD workflow. Do check out some literature for REMD simulations similar to your system. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing 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] The equilibrium before REMD simulations
On 15/11/2011 11:55 AM, ÏéÇ« ¿× wrote: Thanks for everyone's prompt reply! However, i still puzzled why we should use NVT rather than NPT in REMD simulation. As we know that isothermal-isobaric ensemble may be more relevant to the realistic experimental conditions. If the highest temperature was no more than 400K ( i think it is not very high) and the pressure coupling may still work, should NPT be a better choice? Or the NPT method would impair the physical meanings of REMD, however, some NPT examples were depicted in some papers and also in our mailing list. Yes, NPT REMD appears to be quite sound. However, unless you actually want to make measurements of physical observables at the higher temperatures, there's no requirement that the higher ensembles correspond to any particular physical model - see things like resolution replica-exchange. A coordinate mapping, a sufficiency of PE overlap and the possibility of barrier crossing are all that is required for useful replica exchange. There are also some technical issues associated with density in NPT. Because the lists of non-bonded interactions are shorter when the density is lower, the higher-temperature replicas have less work to do, so have to waste some computer time waiting for the lower ones to finish. That's not a big deal, but if you want to use PME and maintain accuracy, the Fourier grid density should change inversely with particle density, and that gets a bit messy. Issues with the size of the integration time step at high P and T have also been known to occur. Mark Best regards! Xiangqian Kong --- On Mon, 11/14/11, Mark Abrahammark.abra...@anu.edu.au wrote: From: Mark Abrahammark.abra...@anu.edu.au Subject: Re: [gmx-users] The equilibrium before REMD simulations To: Discussion list for GROMACS usersgmx-users@gromacs.org Date: Monday, November 14, 2011, 11:53 PM On 15/11/2011 2:50 AM, ÏéÇ« ¿× wrote: Dear Justin, Thanks for your prompt reply! As you say, we should equilibrium each replica at its initial target temperature. So i guess we may do the followings: First, after the minimization and heating, we use NPT to equilibrium the density of the system. And then with the same initial system,equilibrium every replica at their target temperature with NVT ensemble to avoid the instability during REMD and keep the volume constant among the replicas. Finally, do the REMD simulations. Is this workflow reasonable enough and do you have any better guide? Any suggestions will be greatly appreciated! That is a standard REMD workflow. Do check out some literature for REMD simulations similar to your system. 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 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: Questionable van der waals volumes from g_sas
Sorry, ignore my last post, only just realised you had set your probe to 0 radius. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Jacob Alan Spooner Sent: Tuesday, 15 November 2011 11:29 AM To: gmx-users@gromacs.org Subject: [gmx-users] Questionable van der waals volumes from g_sas Hello gmx-users I have been attempting to obtain van der Waal's volumes using the g_sas utility. The command I use to do so is something like g_sas -f hexane.gro -s topol.tpr -probe 0 -tv V_vdw.xvg This seems to give reasonable results for most of my test systems, however when I run the command on an optimized structure of cyclohexane I get a larger van der Waal's volume than that of n-hexane. I think this has to do with the fact that the surface calculation method used in g_sas is missing the void in the centre of the ring. In order to test this I increased the size of the ring, calculating the volumes of icosane and cycloicosane. I found that in this case the volume of the cyclic molecule was expectedly smaller. I tried increasing the number of dots used to draw the dot-surface but saw no significant change in the volumes. Therefore my question is if anybody is familiar enough with g_sas to help me understand why the surface calculation method is not giving sensible values for these smaller ring systems. Also I am wondering if anybody can suggest any other free software that would allow me to compute van der Waal's and Solvent Excluded volumes. Thanks in advance. Jake Spooner -- 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: Questionable van der waals volumes from g_sas
Jake, Wont the volume be a function of the probe radius that is used? And hence, if it is too big to fit through the ring, the volume will be larger than if the chain was straight? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Jacob Alan Spooner Sent: Tuesday, 15 November 2011 11:29 AM To: gmx-users@gromacs.org Subject: [gmx-users] Questionable van der waals volumes from g_sas Hello gmx-users I have been attempting to obtain van der Waal's volumes using the g_sas utility. The command I use to do so is something like g_sas -f hexane.gro -s topol.tpr -probe 0 -tv V_vdw.xvg This seems to give reasonable results for most of my test systems, however when I run the command on an optimized structure of cyclohexane I get a larger van der Waal's volume than that of n-hexane. I think this has to do with the fact that the surface calculation method used in g_sas is missing the void in the centre of the ring. In order to test this I increased the size of the ring, calculating the volumes of icosane and cycloicosane. I found that in this case the volume of the cyclic molecule was expectedly smaller. I tried increasing the number of dots used to draw the dot-surface but saw no significant change in the volumes. Therefore my question is if anybody is familiar enough with g_sas to help me understand why the surface calculation method is not giving sensible values for these smaller ring systems. Also I am wondering if anybody can suggest any other free software that would allow me to compute van der Waal's and Solvent Excluded volumes. Thanks in advance. Jake Spooner -- 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] No locks available.
On Mon, Nov 14, 2011 at 7:47 AM, Roland Schulz rol...@utk.edu wrote: Hi, Well, thanks, here comes the questions you asked before. what file system is this? What operating system on the compute node? In case it is a network file system what file system is used underneath and what operating system is the file server using? What version of GROMACS are you using? CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz Memory: 114GB RAM HDD Size: 744GB OS: CentOS 4 (64-bits) 2.6.9-42.0.10.ELlargesmp #1 SMP Tue Feb 27 09:59:08 EST 2007 x86_64 x86_64 x86_64 GNU/Linux Gromacs, VERSION 4.5.3 If you need more information, please feel free to let me know. Best regards, As you workaround you should be able to run with mdrun -noappend. Roland On Sun, Nov 13, 2011 at 10:43 AM, lina lina.lastn...@gmail.com wrote: Hi, This is the first time I met: Fatal error: Failed to lock: md.log. No locks available the disk is not saturated, md.log is normal, The job was stopped months ago, and now I planned to resume it with all the necessary files kept intact. Thanks for pointing out which parts I should examine, Best regards, -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing 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] how to select option for genion command automatically?
I am wondering if there is a flag to make the command select SOL automatically instead of pressing some number each time? I have thousands of structures, it is really time-consuming to select one by one. -- Best, Liang Liu -- 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] how to select option for genion command automatically?
Liu, Liang wrote: I am wondering if there is a flag to make the command select SOL automatically instead of pressing some number each time? I have thousands of structures, it is really time-consuming to select one by one. Yes, there is: http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts -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] how to select option for genion command automatically?
This is what you are looking for: http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts?highlight=scripting Terry On Tue, Nov 15, 2011 at 11:42 AM, Liu, Liang liu4...@gmail.com wrote: I am wondering if there is a flag to make the command select SOL automatically instead of pressing some number each time? I have thousands of structures, it is really time-consuming to select one by one. -- Best, Liang Liu -- 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
Re: [gmx-users] how to select option for genion command automatically?
Yes, I found it. THanks. On Mon, Nov 14, 2011 at 9:45 PM, Terry terrence...@gmail.com wrote: This is what you are looking for: http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts?highlight=scripting Terry On Tue, Nov 15, 2011 at 11:42 AM, Liu, Liang liu4...@gmail.com wrote: I am wondering if there is a flag to make the command select SOL automatically instead of pressing some number each time? I have thousands of structures, it is really time-consuming to select one by one. -- Best, Liang Liu -- 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 -- Best, Liang Liu -- 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] Positive potential energy for TFE solvent
Hi I am still stuck with same problem of obtaining positive potential energy. On 11/11/2011 5:07 PM, Harpreet Basra wrote: Hi I am trying to generate an equilibrated box of 216 TFE molecules.To generate the 216 TFE molecule box i performed following steps: A suggested workflow can be found here http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation I have been following this link only. 1) I got the tfe.gro file and created a cubic box of edge length = 0.516 nm containing 1 TFE molecule (at its center), using the following command: editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516 I chose this length because in the tfe.gro file dimensions of the TFE molecule are 0.516 0.516 0.516. That's not a good reason. Choose a volume and shape that makes sense for your target density. Cubic probably doesn't make sense when a rectangular shape is possible. Then you'll probably want to choose -nbox differently later. I chose a rectangular box too. still i get a positive value for PE and moreover all the molecules move towards two opposite walls of the box. I am not sure that the way I am using the genconf command is the correct way. because I have tried every other possibility for not getting a positive potential, with no success. So here are my .gro file and the topology file for TFE. *tfe.gro file* 7 1TFE F1T 1 0.444 0.344 0.246 1TFE CT 2 0.334 0.245 0.246 1TFE F2T3 0.350 0.160 0.364 1TFE F3T4 0.350 0.160 0.127 1TFE CH2T 5 0.187 0.326 0.246 1TFE OT 6 0.075 0.220 0.246 1TFE HT 7 -0.019 0.266 0.246 0.49174 0.49174 0.49174 topology file [ moleculetype ] ; Name nrexcl TFE 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 FTFE1 TFE F1T 1 -0.170 18.9984 2 CTFE1 TFE CT10.452 12.0110 3 FTFE1 TFE F2T 1 -0.170 18.9984 4 FTFE1 TFE F3T 1 -0.170 18.9984 5 CHTFE 1 TFE CH2T 10.273 14.0270 6 OTFE 1 TFE OT 1 -0.625 15.9994 7 H 1 TFE HT 1 0.410 1.0080 [ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3 2 5 2 0.153 715.0 0.153 715.0 ; C1 C2 5 6 2 0.143 818.0 0.143 818.0 ; C2 O 6 7 2 0.100 1570.0 0.100 1570.0 ; O H [ pairs ] ; ai aj fu c0, c1, ... 1 6 1 ; F1 O 2 7 1 ; C1 H 3 6 1 ; F2 O 4 6 1 ; F3 O [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H and to construct a box of TFE solvent i took the tfe.gro file and replicated the TFE molecule by using genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6 can u plz suggest is it that I am using genconf in a wrong way that it is causing this problem? I am not sure how many molecules (-nbox option in genconf) should i keep in the box in order to get a mass density of 1383g/L for TFE. thanks Harpreet 2) Then using genconf command i replicated the box to get a bigger box with 216 TFE molecules using the following command: genconf -f tfe_box.gro -o out.gro -rot -nbox 6 3) Energy minimization was done using STEEPEST descent 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns NPT (300K, 1atm) equilibration. After doing all these steps still I obtain a positive a potentail energy. I get positive potential energy of the system (2.45+E04 kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive total energy of the system. My question is whether obtaining positive potential energy indicate some error in my TFE solvent box ? Is it because of large Fluorine atoms of TFE ? Does it mean its not properly equilibrated ? What can I do to equilibrate it? You probably have atomic overlaps from your choice of cubic 0.516 box earlier. Did you look at the results of genconf before computing with them? 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] Positive potential energy for TFE solvent
On 15/11/2011 6:06 PM, Harpreet Basra wrote: Hi I am still stuck with same problem of obtaining positive potential energy. On 11/11/2011 5:07 PM, Harpreet Basra wrote: Hi I am trying to generate an equilibrated box of 216 TFE molecules.To generate the 216 TFE molecule box i performed following steps: A suggested workflow can be found here http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation I have been following this link only. 1) I got the tfe.gro file and created a cubic box of edge length = 0.516 nm containing 1 TFE molecule (at its center), using the following command: editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516 I chose this length because in the tfe.gro file dimensions of the TFE molecule are 0.516 0.516 0.516. That's not a good reason. Choose a volume and shape that makes sense for your target density. Cubic probably doesn't make sense when a rectangular shape is possible. Then you'll probably want to choose -nbox differently later. I chose a rectangular box too. still i get a positive value for PE and moreover all the molecules move towards two opposite walls of the box. I am not sure that the way I am using the genconf command is the correct way. because I have tried every other possibility for not getting a positive potential, with no success. So here are my .gro file and the topology file for TFE. *tfe.gro file* 7 1TFE F1T 1 0.444 0.344 0.246 1TFE CT 2 0.334 0.245 0.246 1TFE F2T3 0.350 0.160 0.364 1TFE F3T4 0.350 0.160 0.127 1TFE CH2T 5 0.187 0.326 0.246 1TFE OT 6 0.075 0.220 0.246 1TFE HT 7 -0.019 0.266 0.246 0.49174 0.49174 0.49174 topology file [ moleculetype ] ; Name nrexcl TFE 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 FTFE1 TFE F1T 1 -0.170 18.9984 2 CTFE1 TFE CT10.452 12.0110 3 FTFE1 TFE F2T 1 -0.170 18.9984 4 FTFE1 TFE F3T 1 -0.170 18.9984 5 CHTFE 1 TFE CH2T 10.273 14.0270 6 OTFE 1 TFE OT 1 -0.625 15.9994 7 H 1 TFE HT 1 0.410 1.0080 [ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3 2 5 2 0.153 715.0 0.153 715.0 ; C1 C2 5 6 2 0.143 818.0 0.143 818.0 ; C2 O 6 7 2 0.100 1570.0 0.100 1570.0 ; O H [ pairs ] ; ai aj fu c0, c1, ... 1 6 1 ; F1 O 2 7 1 ; C1 H 3 6 1 ; F2 O 4 6 1 ; F3 O [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H and to construct a box of TFE solvent i took the tfe.gro file and replicated the TFE molecule by using genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6 can u plz suggest is it that I am using genconf in a wrong way that it is causing this problem? I am not sure how many molecules (-nbox option in genconf) should i keep in the box in order to get a mass density of 1383g/L for TFE. That link says Work out how much volume a single molecule would have in the box of your chosen density and size. Useeditconf http://www.gromacs.org/editconfto place a box of that size around your single molecule. It does not seem to me that you have done this. Mark thanks Harpreet 2) Then using genconf command i replicated the box to get a bigger box with 216 TFE molecules using the following command: genconf -f tfe_box.gro -o out.gro -rot -nbox 6 3) Energy minimization was done using STEEPEST descent 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns NPT (300K, 1atm) equilibration. After doing all these steps still I obtain a positive a potentail energy. I get positive potential energy of the system (2.45+E04 kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive total energy of the system. My question is whether obtaining positive potential energy indicate some error in my TFE solvent box ? Is it because of large Fluorine atoms of TFE ? Does it mean its not properly equilibrated ? What can I do to equilibrate it? You probably have atomic overlaps from your choice of cubic 0.516 box earlier. Did you look at the results of genconf before computing with them? 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
[gmx-users] Re: Positive potential energy for TFE solvent
hi, I am still stuck with same problem of obtaining positive potential energy. On 11/11/2011 5:07 PM, Harpreet Basra wrote: Hi I am trying to generate an equilibrated box of 216 TFE molecules.To generate the 216 TFE molecule box i performed following steps: A suggested workflow can be found here http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation I have been following this link only. 1) I got the tfe.gro file and created a cubic box of edge length = 0.516 nm containing 1 TFE molecule (at its center), using the following command: editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516 I chose this length because in the tfe.gro file dimensions of the TFE molecule are 0.516 0.516 0.516. That's not a good reason. Choose a volume and shape that makes sense for your target density. Cubic probably doesn't make sense when a rectangular shape is possible. Then you'll probably want to choose -nbox differently later. I chose a rectangular box too. still i get a positive value for PE and moreover all the molecules move towards two opposite walls of the box. I am not sure that the way I am using the genconf command is the correct way. because I have tried every other possibility for not getting a positive potential, with no success. So here are my .gro file and the topology file for TFE. the energy of this one molecule (tfe.gro) was coming out to b e highly negative (-6.4E+08 kJ/mol). But on generating a solvent system with 216 molecules the energy becomes (1.9E+04 kJ/mol). **tfe.gro file* 7 1TFE F1T 1 0.444 0.344 0.246 1TFE CT 2 0.334 0.245 0.246 1TFE F2T3 0.350 0.160 0.364 1TFE F3T4 0.350 0.160 0.127 1TFE CH2T 5 0.187 0.326 0.246 1TFE OT 6 0.075 0.220 0.246 1TFE HT 7 -0.019 0.266 0.246 0.49174 0.49174 0.49174 topology file [ moleculetype ] ; Name nrexcl TFE 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 FTFE1 TFE F1T 1 -0.170 18.9984 2 CTFE1 TFE CT10.452 12.0110 3 FTFE1 TFE F2T 1 -0.170 18.9984 4 FTFE1 TFE F3T 1 -0.170 18.9984 5 CHTFE 1 TFE CH2T 10.273 14.0270 6 OTFE 1 TFE OT 1 -0.625 15.9994 7 H 1 TFE HT 1 0.410 1.0080 [ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3 2 5 2 0.153 715.0 0.153 715.0 ; C1 C2 5 6 2 0.143 818.0 0.143 818.0 ; C2 O 6 7 2 0.100 1570.0 0.100 1570.0 ; O H [ pairs ] ; ai aj fu c0, c1, ... 1 6 1 ; F1 O 2 7 1 ; C1 H 3 6 1 ; F2 O 4 6 1 ; F3 O [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H To construct a box of TFE solvent i took the tfe.gro file and replicated the TFE molecule by using genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6 can u plz suggest is it that I am using genconf in a wrong way that it is causing this problem? I am not sure how many molecules (-nbox option in genconf) should i keep in the box in order to get a mass density of 1383g/L for TFE. Though i checked the denity of solvent box i constructed the average valu comes out to be 1397g/L with a std deviation of 30g/L. thus it seems range. thanks Harpreet 2) Then using genconf command i replicated the box to get a bigger box with 216 TFE molecules using the following command: genconf -f tfe_box.gro -o out.gro -rot -nbox 6 3) Energy minimization was done using STEEPEST descent 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns NPT (300K, 1atm) equilibration. After doing all these steps still I obtain a positive a potentail energy. I get positive potential energy of the system (2.45+E04 kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive total energy of the system. My question is whether obtaining positive potential energy indicate some error in my TFE solvent box ? Is it because of large Fluorine atoms of TFE ? Does it mean its not properly equilibrated ? What can I do to equilibrate it? You probably have atomic overlaps from your choice of cubic 0.516 box earlier. Did you look at the results of genconf before computing with them? 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
