[gmx-users] how to build xtc file from many same crystal structures which are different conformational states.
Dear gmx-users： I want to analysis PCA for many crystal strcutures, comparing with MD trajectories, but how to build xtc file from many same structures whchi are different conforamtional states. thank you 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
Re: [gmx-users] how to build a mixed lipid bilayer?
Dear Mr Li Thank you for your help! Can you tell me more detials for the first step, for example, entire command line? thank you! Best regards! --- 12年7月29日，周日, Jianguo Li ljg...@yahoo.com.sg 写道： 发件人: Jianguo Li ljg...@yahoo.com.sg 主题: Re: [gmx-users] how to build a mixed lipid bilayer? 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年7月29日,周日,下午6:29 There are several ways, usually I do like the following: 1. first construct one leaflet. Use editconf -translate to construct a small box containing with 3 POPE 1 POPE 2. Use genconf -nbox to replicate the above in x,y dimension to get 64 lipids 3. Use editconf -rotate -translate to get the another leaflet with 64 lipids 4. Use cat to conbine the two leaflet 5. Use grep and cat commands to re-order the lipids. 6. Change the z dimension of the box. Also change vdwradii.dat and solvate the system and add counter ions. After that run a long simulation to equilibrate the system. btw, which force field you want? If you use gromos force field, you can download the itp and pdb files from http://www.softsimu.net/downloads.shtml If you want CHARMM36, I can send you the files. -Jianguo From: xi zhao zhaoxiitc2...@yahoo.com.cn To: gmx-users@gromacs.org Sent: Sunday, 29 July 2012, 9:19 Subject: [gmx-users] how to build a mixed lipid bilayer? Dear Users: I would like to build a mixed lipid bilayer (POPE/POPG=3:1) in the MD using Gromacs, please provide some tools for producing the structures or existing structures (PDB or gro files). Thank you very much! -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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 build a mixed lipid bilayer?
Dear Users: I would like to build a mixed lipid bilayer (POPE/POPG=3:1) in the MD using Gromacs, please provide some tools for producing the structures or existing structures (PDB or gro files). Thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 1
Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Thank you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 1
in fact, the program hang. --- 12年6月3日，周日, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Atomtype 1
in fact, the pdb2gmx still hang. I modified the atomtypes.atp , aminoacids.rtp , ffbonded.itp, ffnonbonded.itp , aminoacids.hdb, residuetypes.dat ,morever, now the pdb2gmx_d even does not the standard protein structure. --- 12年6月3日，周日, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Atomtype 1
I use Ultraedit to produce new part and paste the files; we add a residue name and corresponding atom type and interaction parameters --- 12年6月3日，周日, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Atomtype 1
in windows , I use ultraedit, in linux ,use vi --- 12年6月3日，周日, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午9:19 On 6/3/12 9:16 AM, xi zhao wrote: I use Ultraedit to produce new part and paste the files; we add a residue name and corresponding atom type and interaction parameters Having never used a commercial text editor, I don't know if its integrity. What happens if you use a different editor, like vi/emacs (Linux/Mac) or Notepad (Windows)? What operating system are you using? The only times I've had pdb2gmx die when reading atom types are when the line endings are bad, so I would strongly suspect this is your issue. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *12年6月3日，周日, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://cn.mc151.mail.yahoo.com/mc/compose?to=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 http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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] Atomtype 1
OK, we find the bug. several words have problem of Uppercase and lowercase. thank you very much! --- 12年6月3日，周日, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午9:19 On 6/3/12 9:16 AM, xi zhao wrote: I use Ultraedit to produce new part and paste the files; we add a residue name and corresponding atom type and interaction parameters Having never used a commercial text editor, I don't know if its integrity. What happens if you use a different editor, like vi/emacs (Linux/Mac) or Notepad (Windows)? What operating system are you using? The only times I've had pdb2gmx die when reading atom types are when the line endings are bad, so I would strongly suspect this is your issue. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *12年6月3日，周日, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://cn.mc151.mail.yahoo.com/mc/compose?to=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 http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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
[gmx-users] Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for
Dear gmx-users: When I try to simulation a system: protein + ligand molecule using the Implicit Solvent method. the parameters of Ligand were produced by acpype, but when grompped, the appeared Velocities were taken from a Maxwell distribution at 300 K GB parameter(s) missing or negative for atom type 'o' GB parameter(s) missing or negative for atom type 'os' GB parameter(s) missing or negative for atom type 'c' GB parameter(s) missing or negative for atom type 'c3' GB parameter(s) missing or negative for atom type 'hc' GB parameter(s) missing or negative for atom type 'h1' --- Program grompp_d, VERSION 4.5.3 Source code file: grompp.c, line: 1123 Fatal error: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 6 atomtypes or they might be negative. when I modified amber99sbr.ff/gbsa.itp by adding the atomtype of ligand, the problem is still the same, please give me some suggestions Thank you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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]
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] orca question and LA
Dear Sir: I want to know version of groamcs and orca in your the qm/mm calculation? are they in parallel ? thank you! --- 11年11月10日，周四, Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 写道： 发件人: Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 主题: Re: [gmx-users] orca question and LA 收件人: gmx-users@gromacs.org 日期: 2011年11月10日,周四,下午7:35 I hope you mean ./configure --with-qmmm-orca --without-qmmm-gaussian etc. http://wwwuser.gwdg.de/%7Eggroenh/qmmm.html http://www.dddc.ac.cn/embo04/practicals/qmmm/qmmmvacuum.html www.google.com etc. For MPI, I can't really say as I did not get qm/mm with orca/gmx to run in parallel yet (using cp2k atm). Maybe someone else can advise you. Cheers, Micha On 10/11/11 10:49, xi zhao wrote: I install gmx : ./configure --without-qmmm-orca --without-qmmm-gaussian --enable-mpi then make make install are it right? --- 11年11月10日，周四, Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 写道： 发件人: Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 主题: Re: [gmx-users] orca question and LA 收件人: gmx-users@gromacs.org 日期: 2011年11月10日,周四,下午4:47 Hey there, my last mail got stuck as it was a bit too large it seems. As I wrote earlier there should be NO coordinates in the infofile... It looks like you have a problem with gmx not preparing a correct .inp file which should include keywords from the infofile, the coordinates of the QMsubsystem and pointcharges (depending on the method you use). Are you sure everything is compiled correct and that you specified your virtual atoms correctly for your force field (and with correct positions/constrains)? Have a look if gmx actually creates an .inp file and if yes what it includes. Again, you should go through Gerrit's tutorials, they should get you going. There are also instructions on how to set up LAs for different force fields. Cheers, Micha On 10/11/11 01:19, xi zhao wrote: Dear Sir: How to write a correct BASENAME.ORCAINFO file? According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given.” It means that BASENAME.ORCAINFO may not contain coordinates of QMatoms part, but when groamcs-ORCA runs , it has errors: Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' No atoms to convert in Cartesian2Internal ; When BASENAME.ORCAINFO has coordinates of QMatoms part, ORCA cannot recognizes the LA (gromacs dummy atom) in the QMatoms , how to deal with LA , delete LA in the BASENAME.ORCAINFO? In fact, the stand-alone version of Orca can normally calculates it. Of course, LA must modified! Kind regards! -下面为附件内容- -- 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 -下面为附件内容- -- 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] orca question and LA
I install gmx : ./configure --without-qmmm-orca --without-qmmm-gaussian --enable-mpi then make make install are it right? --- 11年11月10日，周四, Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 写道： 发件人: Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 主题: Re: [gmx-users] orca question and LA 收件人: gmx-users@gromacs.org 日期: 2011年11月10日,周四,下午4:47 Hey there, my last mail got stuck as it was a bit too large it seems. As I wrote earlier there should be NO coordinates in the infofile... It looks like you have a problem with gmx not preparing a correct .inp file which should include keywords from the infofile, the coordinates of the QMsubsystem and pointcharges (depending on the method you use). Are you sure everything is compiled correct and that you specified your virtual atoms correctly for your force field (and with correct positions/constrains)? Have a look if gmx actually creates an .inp file and if yes what it includes. Again, you should go through Gerrit's tutorials, they should get you going. There are also instructions on how to set up LAs for different force fields. Cheers, Micha On 10/11/11 01:19, xi zhao wrote: Dear Sir: How to write a correct BASENAME.ORCAINFO file? According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given.” It means that BASENAME.ORCAINFO may not contain coordinates of QMatoms part, but when groamcs-ORCA runs , it has errors: Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' No atoms to convert in Cartesian2Internal ; When BASENAME.ORCAINFO has coordinates of QMatoms part, ORCA cannot recognizes the LA (gromacs dummy atom) in the QMatoms , how to deal with LA , delete LA in the BASENAME.ORCAINFO? In fact, the stand-alone version of Orca can normally calculates it. Of course, LA must modified! Kind regards! -下面为附件内容- -- 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
回复： [gmx-users] Re: 6. ORCA and dummy atom in the gromacs (xi zhao)
Dear sir: this is my BASENAME.ORCAINFO: ! rks b3lyp svp tightscf opt grid4 nofinalgrid ! normalprint ! rijcosx sv/j *xyz -1 2 S 2.983 3.527 3.279 C 3.007 3.497 3.463 C 3.156 3.478 3.230 C 3.174 3.484 3.088 O 3.236 3.446 3.317 C 3.296 3.455 3.037 C 3.338 3.447 2.901 C 3.473 3.421 2.865 C 3.520 3.429 2.736 C 3.426 3.460 2.629 C 3.291 3.474 2.666 C 3.248 3.466 2.795 H 3.102 3.541 3.489 H 2.938 3.561 3.515 LA 3.005 3.402 3.492 H 3.094 3.510 3.023 H 3.375 3.437 3.113 H 3.543 3.399 2.942 H 3.623 3.409 2.711 O 3.460 3.469 2.507 H 3.223 3.491 2.585 H 3.143 3.475 2.810 * in fact, the stand-alone version of Orca can normal calculates it, of course, LA must be replaced by DA ( dummy atom in ORCA), but if use LA in gromacs/ORCA, Unless this is specifically allowed this means that the basis set is not available for this element - Aborting the run --- 11年11月9日，周三, Gerrit Groenhof ggro...@gwdg.de 写道： 发件人: Gerrit Groenhof ggro...@gwdg.de 主题: [gmx-users] Re: 6. ORCA and dummy atom in the gromacs (xi zhao) 收件人: gmx-users@gromacs.org 日期: 2011年11月9日,周三,下午3:30 Did you run also your QM subsystem with the stand-alone version of Orca? 6. ORCA and dummy atom in the gromacs (xi zhao) Gerrit -- 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] orca question and LA
Dear Sir: How to write a correct BASENAME.ORCAINFO file? According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given.” It means that BASENAME.ORCAINFO may not contain coordinates of QMatoms part, but when groamcs-ORCA runs , it has errors: Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' No atoms to convert in Cartesian2Internal ; When BASENAME.ORCAINFO has coordinates of QMatoms part, ORCA cannot recognizes the LA (gromacs dummy atom) in the QMatoms , how to deal with LA , delete LA in the BASENAME.ORCAINFO? In fact, the stand-alone version of Orca can normally calculates it. Of course, LA must modified! Kind 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
Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
When BASENAME.ORCAINFO has no coordinates of QMatoms, the mdrun showns Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision) Loaded with Money QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 22 QMlevel: RHF/3-21G /home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131... orca initialised... Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water' 500 steps, 0.5 ps. Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' No atoms to convert in Cartesian2Internal When BASENAME.ORCAINFO has coordinates of QMatoms, such as !RKS BP RI SV(P) SV/J TightSCF Opt * xyz -1 2 O 29.830 35.270 32.790 H 30.070 34.970 34.630 C 31.560 34.780 32.300 LA 31.740 34.840 30.880 ... mdrun shows :Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision) Loaded with Money QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 22 QMlevel: RHF/3-21G /home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131... 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.1# starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water' 500 steps, 0.5 ps. Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' Unless this is specifically allowed this means that the basis set is not available for this element - Aborting the run --- Program mdrun_p, VERSION 4.5.3 Source code file: qm_orca.c, line: 409 Fatal error: Call to '/home/user/orca_x86_64_exe_r2131/orca pyp_qm how to write the BASENAME.ORCAINFO? how to deal with LA ? --- 11年11月8日，周二, Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 写道： 发件人: Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 主题: Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao) 收件人: gmx-users@gromacs.org 日期: 2011年11月8日,周二,下午4:19 I am not sure I understand exactly what you mean but this is all covered in Gerrit's QM/MM tutorials, I'd recommend you go through those. In the ORCA files there is no need to do anything with LAs, GMX will hand a file with the QMsubsystem to ORCA which includes the LA as hydrogens in your case I guess. Cheers, Micha On 08/11/11 07:07, xi zhao wrote: Thank you for your suggest, my gromacs reinstalled: ./configure -- --without-qmmm-gaussian --without-qmmm-orca when mpirun -np 1 mdrun_p -v -s pyp_qm.tpr, Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision) Loaded with Money QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 22 QMlevel: RHF/3-21G /home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131... 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.1# starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water' 500 steps, 0.5 ps. Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' Unless this is specifically allowed this means that the basis set is not available for this element - Aborting the run --- Program mdrun_p, VERSION 4.5.3 Source code file: qm_orca.c, line: 409 Fatal error: Call to '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' failed .. but a question raised: how to deal with LA in the QMatoms in orca inputfile? using DA ( dummy atom in the ORCA) repaces LA in the QMatoms in the gromacs ? please give me a suggestion! Thank you! --- 11年11月7日，周一, Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 写道： 发件人: Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 主题: Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao) 收件人: gmx-users@gromacs.org 日期: 2011年11月7日,周一,下午10:50 From the output it looks like you forgot the --without-qmmm-gaussian flag while compiling. Micha On 07/11/11 14:42, xi zhao wrote: When remove these lines, the errros still :Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods; when put something there, ( QMmethod =rhf;QMbasis =sto-3g), grompp_a -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr -maxwarn 10 mpirun -np 8 mdrun_a -v -s pyp_qm.tpr .. Back Off! I just backed up md.log to ./#md.log.7# Getting Loaded... Reading file pyp_qm.tpr, VERSION 4.5.3 (double 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. there we go! 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
[gmx-users] ORCA and dummy atom in the gromacs
According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. When BASENAME.ORCAINFO has no coordinates of QMatoms, the mdrun showns Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision) Loaded with Money QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 22 QMlevel: RHF/3-21G /home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131... orca initialised... Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water' 500 steps, 0.5 ps. Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' No atoms to convert in Cartesian2Internal ……… When BASENAME.ORCAINFO has coordinates of QMatoms, such as !RKS BP RI SV(P) SV/J TightSCF Opt * xyz -1 2 O 29.830 35.270 32.790 H 30.070 34.970 34.630 C 31.560 34.780 32.300 LA 31.740 34.840 30.880 ... mdrun shows :Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision) Loaded with Money QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 22 QMlevel: RHF/3-21G /home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131... 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.1# starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water' 500 steps, 0.5 ps. Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' Unless this is specifically allowed this means that the basis set is not available for this element - Aborting the run --- Program mdrun_p, VERSION 4.5.3 Source code file: qm_orca.c, line: 409 Fatal error: Call to '/home/user/orca_x86_64_exe_r2131/orca pyp_qm how to write the BASENAME.ORCAINFO? how to deal with LA in the gromacs for ORCA calculation? -- 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 qm/mm
Dear all users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS B3LYP/G SV(P) TightSCF Opt here is the md file: integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system emtol = 100.0 emstep = 0.001 nstcgsteep = 50 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 nstenergy = 1 nstxtcout = 1 xtc_grps = system energygrps = QMatoms rest_Protein SOL nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = cut-off rcoulomb = 1.4 epsilon_r = 1 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = rest_Protein SOL QMatoms tau_t = 0.1 0.1 0 ; QM atoms are uncoupled ref_t = 300 300 300 Pcoupl = Berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 free_energy = no init_lambda = 0 delta_lambda = 0 QMMM = yes QMMM-grps = QMatoms QMmethod = QMbasis = QMMMscheme = normal QMcharge = -1 CASelectrons = CASorbitals = SH = gen_vel = no gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS unconstrained_start = yes shake_tol = 0.0001 lincs_order = 4 lincs_warnangle = 30 morse = no According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored).”, the QMmethod and QMbasis are blank, But When grompp grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr ………. Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods. How to deal with it? Please help me! thank you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 qm/mm
All users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS B3LYP/G SV(P) TightSCF Opt here is the md file: integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system emtol = 100.0 emstep = 0.001 nstcgsteep = 50 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 nstenergy = 1 nstxtcout = 1 xtc_grps = system energygrps = QMatoms rest_Protein SOL nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = cut-off rcoulomb = 1.4 epsilon_r = 1 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = rest_Protein SOL QMatoms tau_t = 0.1 0.1 0 ; QM atoms are uncoupled ref_t = 300 300 300 Pcoupl = Berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 free_energy = no init_lambda = 0 delta_lambda = 0 QMMM = yes QMMM-grps = QMatoms QMmethod = QMbasis = QMMMscheme = normal QMcharge = -1 CASelectrons = CASorbitals = SH = gen_vel = no gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS unconstrained_start = yes shake_tol = 0.0001 lincs_order = 4 lincs_warnangle = 30 morse = no According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored).”, the QMmethod and QMbasis are blank, But When grompp grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr ………. Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods. How to deal with it? Please help me! -- 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
回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
When remove these lines, the errros still :Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods; when put something there, ( QMmethod =rhf;QMbasis =sto-3g), grompp_a -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr -maxwarn 10 mpirun -np 8 mdrun_a -v -s pyp_qm.tpr .. Back Off! I just backed up md.log to ./#md.log.7# Getting Loaded... Reading file pyp_qm.tpr, VERSION 4.5.3 (double 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. there we go! 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: RHF/STO-3G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 - One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a return 0 or exit(0) in your C code before exiting the application. PID 11786 failed on node n0 (127.0.0.1) due to signal 11. how to deal with? --- 11年11月7日，周一, Gerrit Groenhof ggro...@gwdg.de 写道： 发件人: Gerrit Groenhof ggro...@gwdg.de 主题: [gmx-users] Re 1. orca and qm/mm (xi zhao) 收件人: gmx-users@gromacs.org 日期: 2011年11月7日,周一,下午9:23 Try to remove these lines, or put something there. The input is ignored, but since strings are used as input (for use in multui-layer oniom), leaving blank causes an error. Gerrit On 7 Nov 2011, at 14:21, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. orca and qm/mm (xi zhao) -- Message: 1 Date: Mon, 7 Nov 2011 20:54:04 +0800 (CST) From: xi zhao zhaoxiitc2...@yahoo.com.cn Subject: [gmx-users] orca and qm/mm To: gmx-users@gromacs.org Message-ID: 1320670444.82465.yahoomailclas...@web15103.mail.cnb.yahoo.com Content-Type: text/plain; charset=utf-8 All users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS B3LYP/G SV(P) TightSCF Opt here is the md file: integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system emtol = 100.0 emstep = 0.001 nstcgsteep = 50 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 nstenergy = 1 nstxtcout = 1 xtc_grps = system energygrps = QMatoms rest_Protein SOL nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = cut-off rcoulomb = 1.4 epsilon_r = 1 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = rest_Protein SOL QMatoms tau_t = 0.1 0.1 0 ; QM atoms are uncoupled ref_t = 300 300 300 Pcoupl = Berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 free_energy = no init_lambda = 0 delta_lambda = 0 QMMM = yes QMMM-grps = QMatoms QMmethod = QMbasis = QMMMscheme = normal QMcharge = -1 CASelectrons = CASorbitals = SH = gen_vel = no gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS unconstrained_start = yes shake_tol = 0.0001 lincs_order = 4 lincs_warnangle = 30 morse
回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
in addition, how to write ORCAINFO? Is my file right? ! RKS B3LYP/G SV(P) TightSCF Opt or RKS B3LYP/G SV(P) TightSCF Opt --- 11年11月7日，周一, Gerrit Groenhof ggro...@gwdg.de 写道： 发件人: Gerrit Groenhof ggro...@gwdg.de 主题: [gmx-users] Re 1. orca and qm/mm (xi zhao) 收件人: gmx-users@gromacs.org 日期: 2011年11月7日,周一,下午9:23 Try to remove these lines, or put something there. The input is ignored, but since strings are used as input (for use in multui-layer oniom), leaving blank causes an error. Gerrit On 7 Nov 2011, at 14:21, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. orca and qm/mm (xi zhao) -- Message: 1 Date: Mon, 7 Nov 2011 20:54:04 +0800 (CST) From: xi zhao zhaoxiitc2...@yahoo.com.cn Subject: [gmx-users] orca and qm/mm To: gmx-users@gromacs.org Message-ID: 1320670444.82465.yahoomailclas...@web15103.mail.cnb.yahoo.com Content-Type: text/plain; charset=utf-8 All users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS B3LYP/G SV(P) TightSCF Opt here is the md file: integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system emtol = 100.0 emstep = 0.001 nstcgsteep = 50 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 nstenergy = 1 nstxtcout = 1 xtc_grps = system energygrps = QMatoms rest_Protein SOL nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = cut-off rcoulomb = 1.4 epsilon_r = 1 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = rest_Protein SOL QMatoms tau_t = 0.1 0.1 0 ; QM atoms are uncoupled ref_t = 300 300 300 Pcoupl = Berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 free_energy = no init_lambda = 0 delta_lambda = 0 QMMM = yes QMMM-grps = QMatoms QMmethod = QMbasis = QMMMscheme = normal QMcharge = -1 CASelectrons = CASorbitals = SH = gen_vel = no gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS unconstrained_start = yes shake_tol = 0.0001 lincs_order = 4 lincs_warnangle = 30 morse = no According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given. (This also means that QMmethod and QMbasis from the mdp-file are ignored).”, the QMmethod and QMbasis are blank, But When grompp grompp_c -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr ………. Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods. How to deal with it? Please help me! -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2007/8c5c63c5/attachment-0004.html -- -- 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! End of gmx-users Digest, Vol 91, Issue 36 * -- 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
Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)
Thank you for your suggest, my gromacs reinstalled: ./configure -- --without-qmmm-gaussian --without-qmmm-orca when mpirun -np 1 mdrun_p -v -s pyp_qm.tpr, Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file pyp_qm.tpr, VERSION 4.5.3 (double precision) Loaded with Money QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 22 QMlevel: RHF/3-21G /home/user/orca_x86_64_exe_r2131/home/user/orca_x86_64_exe_r2131... 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.1# starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water' 500 steps, 0.5 ps. Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' Unless this is specifically allowed this means that the basis set is not available for this element - Aborting the run --- Program mdrun_p, VERSION 4.5.3 Source code file: qm_orca.c, line: 409 Fatal error: Call to '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' failed .. but a question raised: how to deal with LA in the QMatoms in orca inputfile? using DA ( dummy atom in the ORCA) repaces LA in the QMatoms in the gromacs ? please give me a suggestion! Thank you! --- 11年11月7日，周一, Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 写道： 发件人: Micha Ben Achim Kunze ucbt...@live.ucl.ac.uk 主题: Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao) 收件人: gmx-users@gromacs.org 日期: 2011年11月7日,周一,下午10:50 From the output it looks like you forgot the --without-qmmm-gaussian flag while compiling. Micha On 07/11/11 14:42, xi zhao wrote: When remove these lines, the errros still :Fatal error: Invalid QMMM input: 1 groups 0 basissets and 0 methods; when put something there, ( QMmethod =rhf;QMbasis =sto-3g), grompp_a -f pyp.mdp -c pyp.gro -p pyp.top -n pyp.ndx -o pyp_qm.tpr -maxwarn 10 mpirun -np 8 mdrun_a -v -s pyp_qm.tpr .. Back Off! I just backed up md.log to ./#md.log.7# Getting Loaded... Reading file pyp_qm.tpr, VERSION 4.5.3 (double 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. there we go! 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: RHF/STO-3G number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 - One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a return 0 or exit(0) in your C code before exiting the application. PID 11786 failed on node n0 (127.0.0.1) due to signal 11. how to deal with? --- 11年11月7日，周一, Gerrit Groenhof ggro...@gwdg.de 写道： 发件人: Gerrit Groenhof ggro...@gwdg.de 主题: [gmx-users] Re 1. orca and qm/mm (xi zhao) 收件人: gmx-users@gromacs.org 日期: 2011年11月7日,周一,下午9:23 Try to remove these lines, or put something there. The input is ignored, but since strings are used as input (for use in multui-layer oniom), leaving blank causes an error. Gerrit On 7 Nov 2011, at 14:21, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. orca and qm/mm (xi zhao) -- Message: 1 Date: Mon, 7 Nov 2011 20:54:04 +0800 (CST) From: xi zhao zhaoxiitc2...@yahoo.com.cn Subject: [gmx-users] orca and qm/mm To: gmx-users@gromacs.org Message-ID: 1320670444.82465.yahoomailclas...@web15103.mail.cnb.yahoo.com Content-Type: text/plain; charset=utf-8 All users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS B3LYP/G SV(P) TightSCF Opt here is the md file: integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system emtol
Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?
Yes, the PSF file has NBOND section and the script finished without any errors! But it does not show any bonded! Thank you！ --- 10年5月7日，周五, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2010年5月7日,周五,下午7:10 xi zhao wrote: Yes， I load my coarse-grained PDB ,then load ps as data, but the stucture still was full of points . Is a proper !NBOND section generated in your .psf file? If the script finishes without any errors, the output should be viable. -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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?
It well done! thank you very much! zhao --- 10年5月7日，周五, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2010年5月7日,周五,下午10:15 I discovered the problem. There was a case of pattern matching that wasn't working, so an extra bond was being written between atom 0 and atom 0, which of course is nonsense. Also be advised that the .psf file was mangled anyway, since you had tried to process different topologies (that didn't work), with the end result being concatenation to the .psf file. If you get a non-functional .psf file, delete it, or else top2psf will happily append to your existing .psf file, generating more nonsense. The end result is that I have fixed the script and uploaded a new version here: http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD -Justin xi zhao wrote: thank you for your help! 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年5月7日，周五, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2010年5月7日,周五,下午7:40 xi zhao wrote: Yes, the PSF file has NBOND section and the script finished without any errors! But it does not show any bonded! Thank you！ Can you send me your coordinate file and .psf file (off-list) so I can see if there's anything to diagnose? If you have an NBOND section, the script has done its job and should work. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年5月7日，周五, Justin A. Lemkul /jalem...@vt.edu http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: Gromacs Users' List gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org 日期: 2010年5月7日,周五,下午7:10 xi zhao wrote: Yes， I load my coarse-grained PDB ,then load ps as data, but the stucture still was full of points . Is a proper !NBOND section generated in your .psf file? If the script finishes without any errors, the output should be viable. -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://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ
Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?
Dear Sir : The script require what format for top file? my top file is here: ; ; Example topology file for MARTINI 2.0 ; ; First include the file containing all particle definitions, ; the interaction matrix, plus the topology for water. #include martini_v2.1.itp #include martini_v2.0_ions.itp #include martini_v2.0_lipids.itp #include 3ehz.itp ; Include Position restraint file #ifdef POSRES #include s.itp #endif [ system ] CGprotein ion channel [ molecules ] ; name number Protein 1 POPC 502 W 18934 but run top2psf.pl Cannot open atoms for reading: No such file or directory please help me! --- 10年5月3日，周一, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年5月3日,周一,上午8:08 xi zhao wrote: Dear user: how to show struture or conformation in Martini coarse-grained simulation, using VMD or other? Please give me some suggestion! thank you! What kind of rendering do you want to do? There are some scripts linked below to render bonds in a CG structure. http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD#VMD_and_coarse-grained_simulations -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?
in fact, how to deal with format problem in coarse-grained ? thank you! --- 10年5月6日，周四, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2010年5月6日,周四,上午9:40 xi zhao wrote: Dear Sir : The script require what format for top file? my top file is here: The input is the actual protein topology, not the system topology. -Justin ; ; Example topology file for MARTINI 2.0 ; ; First include the file containing all particle definitions, ; the interaction matrix, plus the topology for water. #include martini_v2.1.itp #include martini_v2.0_ions.itp #include martini_v2.0_lipids.itp #include 3ehz.itp ; Include Position restraint file #ifdef POSRES #include s.itp #endif [ system ] CGprotein ion channel [ molecules ] ; name number Protein 1 POPC 502 W 18934 but run top2psf.pl Cannot open atoms for reading: No such file or directory please help me! 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年5月3日，周一, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年5月3日,周一,上午8:08 xi zhao wrote: Dear user: how to show struture or conformation in Martini coarse-grained simulation, using VMD or other? Please give me some suggestion! thank you! What kind of rendering do you want to do? There are some scripts linked below to render bonds in a CG structure. http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD#VMD_and_coarse-grained_simulations -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- 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://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?
produce input file , in coarse grained , no standard protein top file --- 10年5月6日，周四, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2010年5月6日,周四,上午10:37 xi zhao wrote: in fact, how to deal with format problem in coarse-grained ? What do you mean? -Justin thank you! 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年5月6日，周四, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2010年5月6日,周四,上午9:40 xi zhao wrote: Dear Sir : The script require what format for top file? my top file is here: The input is the actual protein topology, not the system topology. -Justin ; ; Example topology file for MARTINI 2.0 ; ; First include the file containing all particle definitions, ; the interaction matrix, plus the topology for water. #include martini_v2.1.itp #include martini_v2.0_ions.itp #include martini_v2.0_lipids.itp #include 3ehz.itp ; Include Position restraint file #ifdef POSRES #include s.itp #endif [ system ] CGprotein ion channel [ molecules ] ; name number Protein 1 POPC 502 W 18934 but run top2psf.pl Cannot open atoms for reading: No such file or directory please help me! 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年5月3日，周一, Justin A. Lemkul /jalem...@vt.edu http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: Discussion list for GROMACS users gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org 日期: 2010年5月3日,周一,上午8:08 xi zhao wrote: Dear user: how to show struture or conformation in Martini coarse-grained simulation, using VMD or other? Please give me some suggestion! thank you! What kind of rendering do you want to do? There are some scripts linked below to render bonds in a CG structure. http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD#VMD_and_coarse-grained_simulations -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- 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://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to show structure results in Martini coarse-grained simulation?
Dear user: how to show struture or conformation in Martini coarse-grained simulation, using VMD or other? Please give me some suggestion! thank you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] construct CG membrane protein and CG membrane and inflategro.pl
Dear Gromacs users: I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but when carryied EM with Strong POStion REStraint, the protien and membrane were apart. Please help me! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl
protein and membranr separate , --- 10年4月12日，周一, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年4月12日,周一,下午8:42 xi zhao wrote: Dear Gromacs users: I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but when carryied EM with Strong POStion REStraint, the protien and membrane were apart. Please help me! What does apart mean? If you want free help, you have to make it easy to help you. That means thorough descriptions of what you're doing, what you're seeing, and if necessary, posting images online (not as attachments!) for us to take a look. The InflateGRO method should generate a configuration that has molecules separated by a large amount of space, but if there is something else wrong you'll have to provide a better description. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl
my procesure: 1. cat cgprotein cgmembranesystem.gro (using Martini force field) 2 perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat 3. grompp_d -f em.mdp -c system_inflated.gro -p topol.top -o system_inflatedem.tpr (with strong postion restraint) 4. mdrun 5 in the system_inflatedem.gro , the protein and membrane separate each other. please help me ! --- 10年4月12日，周一, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年4月12日,周一,下午8:42 xi zhao wrote: Dear Gromacs users: I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but when carryied EM with Strong POStion REStraint, the protien and membrane were apart. Please help me! What does apart mean? If you want free help, you have to make it easy to help you. That means thorough descriptions of what you're doing, what you're seeing, and if necessary, posting images online (not as attachments!) for us to take a look. The InflateGRO method should generate a configuration that has molecules separated by a large amount of space, but if there is something else wrong you'll have to provide a better description. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl
Dear Sir : In fact, these structures were initially centered within the same coordinate system as your Gromacs Tutorials . --- 10年4月12日，周一, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2010年4月12日,周一,下午9:07 xi zhao wrote: my procesure: 1. cat cgprotein cgmembranesystem.gro (using Martini force field) Were these structures initially centered within the same coordinate system? By your description, it sounds like these two components are simply not placed properly. There is a membrane protein tutorial linked from the Gromacs Tutorials page that guides you through constructing an atomistic membrane protein system using InflateGRO. You might find it useful. -Justin 2 perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat 3. grompp_d -f em.mdp -c system_inflated.gro -p topol.top -o system_inflatedem.tpr (with strong postion restraint) 4. mdrun 5 in the system_inflatedem.gro , the protein and membrane separate each other. please help me ! 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年4月12日，周一, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年4月12日,周一,下午8:42 xi zhao wrote: Dear Gromacs users: I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but when carryied EM with Strong POStion REStraint, the protien and membrane were apart. Please help me! What does apart mean? If you want free help, you have to make it easy to help you. That means thorough descriptions of what you're doing, what you're seeing, and if necessary, posting images online (not as attachments!) for us to take a look. The InflateGRO method should generate a configuration that has molecules separated by a large amount of space, but if there is something else wrong you'll have to provide a better description. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- 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://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] InflateGRO and pentamer protein simulation
Dear sir: Thank you for your help! --- 10年4月11日，周日, shaya...@post.tau.ac.il shaya...@post.tau.ac.il 写道： 发件人: shaya...@post.tau.ac.il shaya...@post.tau.ac.il 主题: Re: [gmx-users] InflateGRO and pentamer protein simulation 收件人: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年4月11日,周日,下午10:01 Dear Xi Zhao, For inserting protein into membrane you might like to try use g_membed (link http://wwwuser.gwdg.de/~ggroenh/membed.html) This is not strictly (yet) a gromacs package, but it can be very easily be complied and used per instructions of the authors. Technically, the package 'compress' the protein to be a linear line, then inserts it into the membrane and starts 'pumping' it back to the original size. Hope that help, -Shay Quoting Justin A. Lemkul jalem...@vt.edu: xi zhao wrote: I would like to run a simulation of a pentamers in a POPC membrane, and using new inflategro with doughnut mode, but I have met similar result as the links http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I also http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I also got a lot of errors about uninitialized values. When the script finishes, the membrane is rescaled, but the protein is untouched in the corner of the new box. Please give me some suggestions! Thank you in advance! best regards! I think the problem comes from pattern matching in the script. With large bilayers, the atom names and numbers will not be split correctly; this could be causing a problem for you. I'd again suggest that you contact the developer of the program and discuss this issue, as it is not really a Gromacs problem and only a few people on this list really use such programs. I think you'll find a resolution faster that way. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年4月9日，周五, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] InflateGRO and pentamer protein simulation 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年4月9日,周五,上午2:14 xi zhao wrote: Dear sir : I want to a pentamer membrane protein, when I used InflateGRO.pl with /DOUGHNUT Mode, the results were wrong, please help me! / If you want any useful help, you'll have to do a whole lot better than simply saying the results were wrong. No one on this list will have any idea what you mean. If you believe there is some error in the script itself, you're better off contacting its author. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844show [u...@localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 14 kk_inflated.gro 5 area.dat doughnut protein_subunits Doughnut mode activated. Protein coordinates will be translated by subunit Reading. Reading chain identifiers Subunit 1: atom 1 to atom 3238 Subunit 2: atom 3239 to atom 6476 Subunit 3: atom 6477 to atom 9714 Subunit 4: atom 9715 to atom 12952 Subunit 5: atom 12953 to atom 16190 There are 5 protein subunits Scaling lipids There are 512 lipids... with 65 atoms per lipid.. Determining upper and lower leaflet... 256 lipids in the upper... 256 lipids in the lower leaflet Checking for overlap ...this might actually take a while... ... Argument N4 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C5 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C6 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O7 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument P8 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O9 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C3 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument N4 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C5 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C6 isn't
[gmx-users] InflateGRO and pentamer protein simulation
Dear sir : I want to a pentamer membrane protein, when I used InflateGRO.pl with DOUGHNUT Mode, the results were wrong, please help me! show [u...@localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 14 kk_inflated.gro 5 area.dat doughnut protein_subunits Doughnut mode activated. Protein coordinates will be translated by subunit Reading. Reading chain identifiers Subunit 1: atom 1 to atom 3238 Subunit 2: atom 3239 to atom 6476 Subunit 3: atom 6477 to atom 9714 Subunit 4: atom 9715 to atom 12952 Subunit 5: atom 12953 to atom 16190 There are 5 protein subunits Scaling lipids There are 512 lipids... with 65 atoms per lipid.. Determining upper and lower leaflet... 256 lipids in the upper... 256 lipids in the lower leaflet Checking for overlap ...this might actually take a while... ... Argument N4 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C5 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C6 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O7 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument P8 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O9 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C3 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument N4 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C5 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C6 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O7 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument P8 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O9 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Calculating Area per lipid... Protein X-min/max: 23 105 Protein Y-min/max: 18 100 X-range: 82 A Y-range: 82 A Building 82 X 82 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 49 nm^2 Area per lipid: 9.83158146861789 nm^2 Area per protein, upper half: 38.75 nm^2 Area per lipid, upper leaflet : 9.79362516645161 nm^2 Area per protein, lower half: 45.75 nm^2 Area per lipid, lower leaflet : 9.92548787409836 nm^2 Writing Area per lipid... Done! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] InflateGRO and pentamer protein simulation
I would like to run a simulation of a pentamers in a POPC membrane, and using new inflategro with doughnut mode, but I have met similar result as the links http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I also got a lot of errors about uninitialized values. When the script finishes, the membrane is rescaled, but the protein is untouched in the corner of the new box. Please give me some suggestions! Thank you in advance! best regards! --- 10年4月9日，周五, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] InflateGRO and pentamer protein simulation 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年4月9日,周五,上午2:14 xi zhao wrote: Dear sir : I want to a pentamer membrane protein, when I used InflateGRO.pl with /DOUGHNUT Mode, the results were wrong, please help me! / If you want any useful help, you'll have to do a whole lot better than simply saying the results were wrong. No one on this list will have any idea what you mean. If you believe there is some error in the script itself, you're better off contacting its author. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844show [u...@localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 14 kk_inflated.gro 5 area.dat doughnut protein_subunits Doughnut mode activated. Protein coordinates will be translated by subunit Reading. Reading chain identifiers Subunit 1: atom 1 to atom 3238 Subunit 2: atom 3239 to atom 6476 Subunit 3: atom 6477 to atom 9714 Subunit 4: atom 9715 to atom 12952 Subunit 5: atom 12953 to atom 16190 There are 5 protein subunits Scaling lipids There are 512 lipids... with 65 atoms per lipid.. Determining upper and lower leaflet... 256 lipids in the upper... 256 lipids in the lower leaflet Checking for overlap ...this might actually take a while... ... Argument N4 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C5 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C6 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O7 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument P8 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O9 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C3 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument N4 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C5 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument C6 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O7 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument P8 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument O9 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A1 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Argument A2 isn't numeric in printf at inflategro.txt line 708, CHAINS line 5. Calculating Area per lipid... Protein X-min/max: 23 105 Protein Y-min/max: 18 100 X-range: 82 A Y-range: 82 A Building 82 X 82 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 49 nm^2 Area per lipid: 9.83158146861789 nm^2 Area per protein, upper half: 38.75 nm^2 Area per lipid, upper leaflet : 9.79362516645161 nm^2 Area per protein, lower half: 45.75 nm^2 Area per lipid, lower leaflet : 9.92548787409836 nm^2 Writing Area per lipid... Done! -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting
[gmx-users] coarse-grained model of POPC in Martini coarse-grained force field?
I'd like to run simulations with coarse grained model lipid bilayer. I can not find the force field for coarse grain POPC lipid or equilibrated bilayer coordinates in Martini website. Please help me! thank you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
Dear gromacs users: How to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations; for example, software or script using, how to reconstruct PMF in detail? thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to analye a single structure (NMR or X-ray) by PCA?
Dear sir : I want to analye a collective motions of a single structure by PCA , for example, how to choose reference structure using g_covar; how to show its position in 2D-projection (conformational space)? thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
dear Mr Justin A. Lemkul : I have read your tutorial ,it is suitable for umbrella sampling method, it is not for SMD, wham or g_wham can not be used! Thnak you! --- 10年3月24日，周三, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年3月24日,周三,下午9:58 xi zhao wrote: Dear gromacs users: How to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations; for example, software or script using, how to reconstruct PMF in detail? thank you very much! http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
Dear Mr Justin A. Lemkul : Thank you for your advice, can you give more suggetions? Thank you very much! --- 10年3月24日，周三, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2010年3月24日,周三,下午10:10 xi zhao wrote: dear Mr Justin A. Lemkul : I have read your _tutorial ,it is suitable for umbrella sampling method, it is not for SMD, wham or g_wham can not be used!_ _Thnak you!_ If you want to use SMD trajectories to calculate free energy changes, you will need Jarzynski's inequality and a large amount of sampling. I do not think such a method is implemented in Gromacs; you may have to write your own scripts to do this. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年3月24日，周三, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年3月24日,周三,下午9:58 xi zhao wrote: Dear gromacs users: How to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations; for example, software or script using, how to reconstruct PMF in detail? thank you very much! http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- 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://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
Dear Mr Justin A. Lemkul : In fact, please read the document http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-513/paper06.pdf, the document shows the PMF can be reconstructed from the SMD, why? thank you! --- 10年3月24日，周三, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2010年3月24日,周三,下午10:10 xi zhao wrote: dear Mr Justin A. Lemkul : I have read your _tutorial ,it is suitable for umbrella sampling method, it is not for SMD, wham or g_wham can not be used!_ _Thnak you!_ If you want to use SMD trajectories to calculate free energy changes, you will need Jarzynski's inequality and a large amount of sampling. I do not think such a method is implemented in Gromacs; you may have to write your own scripts to do this. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年3月24日，周三, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年3月24日,周三,下午9:58 xi zhao wrote: Dear gromacs users: How to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations; for example, software or script using, how to reconstruct PMF in detail? thank you very much! http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- 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://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to analysis crystal structure and 2D projections by PCA?
Dear users: I want to analyse a crystal structure by PCA, and want to show its 2D projection, but I meet errors segment fault my procedure: g_covar_d -f crystal strucutre.pdb -s crystal strucutre.pdb -o eig.xvg -v eig.trr g_anaeig_d -f crystal strucutre.pdb -eig eig.xvg -v eig.trr -2d 2d.xvg -first 1 -last 2 but produce errors. Please help me! thank you! ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection
Dear Mr Tsjerk Wassenaar : Thank you for your advice! I will try it! regards! --- 09年12月23日，周三, Tsjerk Wassenaar tsje...@gmail.com 写道： 发件人: Tsjerk Wassenaar tsje...@gmail.com 主题: Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2009年12月23日,周三,下午7:26 Xi Zhao, I have no script either. It's not my homework, and I'm not on your payroll. If I need a script like that and write it, I'll be happy to share it with you. But that's not going to be soon. At present, I don't even have a data set to use to develop something like it. On the other hand, if you put effort in writing a script for it (you may want to try and learn a bit of python), and get stuck, I'll be happy to reflect on your code, as will others that are on this list. That is how things work here. Cheers, Tsjerk On Wed, Dec 23, 2009 at 2:07 AM, xi zhao zhaoxiitc2...@yahoo.com.cn wrote: Dear Mr Tsjerk Wassenaar : Thank you for your help! I only study on conformation transfromation (transformation) of protein, and need point to corresponding conformation in 2d projection or free energy landscape! I have no any script, please help me! Best regards! --- 09年12月22日，周二, Tsjerk Wassenaar tsje...@gmail.com 写道： 发件人: Tsjerk Wassenaar tsje...@gmail.com 主题: Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2009年12月22日,周二,下午7:43 Ni hao Xi Zhao, Please note again that you're working with projections. There is not necessarily a single conformation that corresponds to the energy minimum from your projection space. You can obtain the minimum from the 2D projection and then find the conformation that yields the projection closest to that point, by taking the Euclidean distance between the projection and the minimum. You'll have to do a bit of scripting there. Cheers, Tsjerk On Mon, Dec 21, 2009 at 2:51 PM, xi zhao zhaoxiitc2...@yahoo.com.cn wrote: Dear Mr Tsjerk Wassenaar ： Thank you for your help! what you said is reasonal, but how to implement them, or detial procedure? The 2d projections can convert to a free energy landscape, and how to obtain conformation in the minimum of energy surface? best regards! --- 09年12月21日，周一, Tsjerk Wassenaar tsje...@gmail.com 写道： 发件人: Tsjerk Wassenaar tsje...@gmail.com 主题: Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2009年12月21日,周一,下午7:57 Ni hao, Since it's a projection, there is not (in general) a single conformation for each point in the 2D plane. On the other hand, the points you obtained are derived from distinct (ordered) conformations, so it is trivial to retrieve them. Each conformation (time) yields one point: find the time for which the point corresponds with the one your interested in, and extract the conformation from the trajectory. Cheers, Tsjerk 2009/12/20 xi zhao zhaoxiitc2...@yahoo.com.cn Dear users for gromacs: We know that observing the sampled conformations in the subspace spanned by the eigenvectors is a so-called two-dimensional projection(2D projection), in 2-D projection, each point represents a snapshot from the simulation, and the distribution shows the sampled region along the first two eigenvectors during the simulation. But I feel confounded, because I do not know to how to obtain corresponding conformation for each point in the 2-D projection.Please help me! best regards! thank you! 好玩贺卡等你发，邮箱贺卡全新上线！ -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -下面为附件内容- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php 好玩贺卡等你发，邮箱贺卡全新上线！ -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist
Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection
Dear Mr Tsjerk Wassenaar : Thank you for your help! I only study on conformation transfromation (transformation) of protein, and need point to corresponding conformation in 2d projection or free energy landscape! I have no any script, please help me! Best regards! --- 09年12月22日，周二, Tsjerk Wassenaar tsje...@gmail.com 写道： 发件人: Tsjerk Wassenaar tsje...@gmail.com 主题: Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2009年12月22日,周二,下午7:43 Ni hao Xi Zhao, Please note again that you're working with projections. There is not necessarily a single conformation that corresponds to the energy minimum from your projection space. You can obtain the minimum from the 2D projection and then find the conformation that yields the projection closest to that point, by taking the Euclidean distance between the projection and the minimum. You'll have to do a bit of scripting there. Cheers, Tsjerk On Mon, Dec 21, 2009 at 2:51 PM, xi zhao zhaoxiitc2...@yahoo.com.cn wrote: Dear Mr Tsjerk Wassenaar ： Thank you for your help! what you said is reasonal, but how to implement them, or detial procedure? The 2d projections can convert to a free energy landscape, and how to obtain conformation in the minimum of energy surface? best regards! --- 09年12月21日，周一, Tsjerk Wassenaar tsje...@gmail.com 写道： 发件人: Tsjerk Wassenaar tsje...@gmail.com 主题: Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2009年12月21日,周一,下午7:57 Ni hao, Since it's a projection, there is not (in general) a single conformation for each point in the 2D plane. On the other hand, the points you obtained are derived from distinct (ordered) conformations, so it is trivial to retrieve them. Each conformation (time) yields one point: find the time for which the point corresponds with the one your interested in, and extract the conformation from the trajectory. Cheers, Tsjerk 2009/12/20 xi zhao zhaoxiitc2...@yahoo.com.cn Dear users for gromacs: We know that observing the sampled conformations in the subspace spanned by the eigenvectors is a so-called two-dimensional projection(2D projection), in 2-D projection, each point represents a snapshot from the simulation, and the distribution shows the sampled region along the first two eigenvectors during the simulation. But I feel confounded, because I do not know to how to obtain corresponding conformation for each point in the 2-D projection.Please help me! best regards! thank you! 好玩贺卡等你发，邮箱贺卡全新上线！ -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -下面为附件内容- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php 好玩贺卡等你发，邮箱贺卡全新上线！ -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -下面为附件内容- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection
Dear Mr Tsjerk Wassenaar ： Thank you for your help! what you said is reasonal, but how to implement them, or detial procedure? The 2d projections can convert to a free energy landscape, and how to obtain conformation in the minimum of energy surface? best regards! --- 09年12月21日，周一, Tsjerk Wassenaar tsje...@gmail.com 写道： 发件人: Tsjerk Wassenaar tsje...@gmail.com 主题: Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2009年12月21日,周一,下午7:57 Ni hao, Since it's a projection, there is not (in general) a single conformation for each point in the 2D plane. On the other hand, the points you obtained are derived from distinct (ordered) conformations, so it is trivial to retrieve them. Each conformation (time) yields one point: find the time for which the point corresponds with the one your interested in, and extract the conformation from the trajectory. Cheers, Tsjerk 2009/12/20 xi zhao zhaoxiitc2...@yahoo.com.cn Dear users for gromacs: We know that observing the sampled conformations in the subspace spanned by the eigenvectors is a so-called two-dimensional projection(2D projection), in 2-D projection, each point represents a snapshot from the simulation, and the distribution shows the sampled region along the first two eigenvectors during the simulation. But I feel confounded, because I do not know to how to obtain corresponding conformation for each point in the 2-D projection.Please help me! best regards! thank you! 好玩贺卡等你发，邮箱贺卡全新上线！ -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -下面为附件内容- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to obtain corresponding conformation for each point in the 2-D projection
Dear users for gromacs: We know that observing the sampled conformations in the subspace spanned by the eigenvectors is a so-called two-dimensional projection(2D projection), in 2-D projection, each point represents a snapshot from the simulation, and the distribution shows the sampled region along the first two eigenvectors during the simulation. But I feel confounded, because I do not know to how to obtain corresponding conformation for each point in the 2-D projection.Please help me! best regards! thank you! ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to plot free enenrgy landscape and exact corresponding conformation
Dear Users of Groamcs: ON the abasis of ED analysis, how to plot free energy landscape and exact corresponding conformation? Thank you very much! ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to perform Combined essential dynamics analysis and procedure!
Dear sir : Can you give me some information on Combined essential dynamics analysis and its procedure? Thank you! ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to use atom2cg.awk
Dear Sir: In fact, I have modified the script as you said, but the CG strucrute produced is not different in secondary strucure with native PDB structure: CG structure became a line strucrue! Please help me! Or give me a good script! Thank you very much! Best regards! --- 09年5月11日，周一, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to use atom2cg.awk 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2009年5月11日,周一,上午8:22 xi zhao wrote: Dear sir : how to motify the $5 in details? Thank you! Use a text editor (vi, emacs, gedit, etc), like you would to create any script. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *09年5月8日，周五, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to use atom2cg.awk 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2009年5月8日,周五,下午6:46 xi zhao wrote: Dear Sirs: I wang to know simulate coarse-graied system using gromacs, but I don not know how to use atom2cg.awk to convert CG model! Thank you very much! ./atom2cg_v2.1_tryout.awk my.pdb out.pdb Note that the script available online needs to be modified to include a $5 between the $4 and $6 on each line, otherwise you will get an incorrectly-formatted .pdb file. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 好玩贺卡等你发，邮箱贺卡全新上线！ http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/ ___ gmx-users mailing list gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php 好玩贺卡等你发，邮箱贺卡全新上线！ http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post
Re: [gmx-users] how to use atom2cg.awk
Dear sir: This is my modified script, please see it! I take CG simulations according to http://md.chem.rug.nl/marrink/coarsegrain.html. Thank you ! --- 09年5月11日，周一, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to use atom2cg.awk 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2009年5月11日,周一,下午6:49 xi zhao wrote: Dear Sir: In fact, I have modified the script as you said, but the CG strucrute produced is not different in secondary strucure with native PDB structure: CG structure became a line strucrue! Please help me! Or give me a good script! Visualization is not an appropriate method to use to determine the validity of your procedure. The CG model will look a bit strange when rendered as lines in most visualization software. You did modify each line of the script, inserting $5 between every $4 and $6, correct? -Justin Thank you very much! Best regards! 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *09年5月11日，周一, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to use atom2cg.awk 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2009年5月11日,周一,上午8:22 xi zhao wrote: Dear sir : how to motify the $5 in details? Thank you! Use a text editor (vi, emacs, gedit, etc), like you would to create any script. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *09年5月8日，周五, Justin A. Lemkul /jalem...@vt.edu http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu 主题: Re: [gmx-users] how to use atom2cg.awk 收件人: Discussion list for GROMACS users gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org 日期: 2009年5月8日,周五,下午6:46 xi zhao wrote: Dear Sirs: I wang to know simulate coarse-graied system using gromacs, but I don not know how to use atom2cg.awk to convert CG model! Thank you very much! ./atom2cg_v2.1_tryout.awk my.pdb out.pdb Note that the script available online needs to be modified to include a $5 between the $4 and $6 on each line, otherwise you will get an incorrectly-formatted .pdb file. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 好玩贺卡等你发，邮箱贺卡全新上线！ http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/ ___ gmx-users mailing list gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
Re: [gmx-users] how to use atom2cg.awk
Dear sir : how to motify the $5 in details? Thank you! --- 09年5月8日，周五, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to use atom2cg.awk 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2009年5月8日,周五,下午6:46 xi zhao wrote: Dear Sirs: I wang to know simulate coarse-graied system using gromacs, but I don not know how to use atom2cg.awk to convert CG model! Thank you very much! ./atom2cg_v2.1_tryout.awk my.pdb out.pdb Note that the script available online needs to be modified to include a $5 between the $4 and $6 on each line, otherwise you will get an incorrectly-formatted .pdb file. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 好玩贺卡等你发，邮箱贺卡全新上线！ http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to use atom2cg.awk
Dear Sirs: I wang to know simulate coarse-graied system using gromacs, but I don not know how to use atom2cg.awk to convert CG model! Thank you very much! ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pull.pdo and AFM force
All users: I want to calculate the AFM force in afm pulling, is there a script to obtain forces from afm pulling! In fact, g_wham can not run, it is very depressed. Please help me! Thank you in advance! - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to fix the center of mass of the protein in the pull simulation
Dear users: how to fix the center of mass of the protein in the pull simulation? I want to know to know! Please help me! - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to fix the COM of group in the pull.
Dear users: I want to know how to fix the com of the group in the pull or afm simulation,Please give some ideas. - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] analysizing the sam.edo script?
Dear users: I want to analyze the EDS (essential dynamics sampling ) results (sam.edo file),though the website and manual both show that parse_edo can do it, I do not know how to get it,because I can not find it in the website. Please help me! - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to fix a position in the single eigenvector in essential dynamics sampling?
Dear users: I want to know: in EDS (essential dynamics sampling), how to fix the eigenvector ,while the other degrees of freedom wiil be equilibrated. how to set up? using the :linfix in make_edi ? Please help me! Thank you very much! - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: 回复： Re: [gmx-use rs] 2D projection and corresponding conformation
Dear sir: For example, I only simulated a protein, further, 1. using g_covar producing eigenvalue.xvg and eigenvec.trr for all Ca atoms 2 using g_anaeig producing 2d projection.xvg 3 how to obtain corresponding corformation in 2d projection using trjconv? these steps are normal, can you give me some advise! ? Thank you very much! Mark Abraham [EMAIL PROTECTED] 写道： xi zhao wrote: Dear sir : I also know these,but can you give some detail procedure for obtaining the corresponding conformations? Thank you in advance! No, because you've told us no detail of your procedure to generate your eigensystem and to produce the (labeled) projected points. Once you've got that, it's probably just a matter of applying trjconv thoughtfully. Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] 2D projection and corresponding conformation
Dear user: We know that observing the sampled conformations in the subspace spanned by the eigenvectors is a so-called two-dimensional projection(2D projection), in 2-D projection, each point represents a snapshot from the simulation, and the distribution shows the sampled region along the first two eigenvectors during the simulation. But I feel confounded, because I do not know to how to obtain corresponding conformation for each point in the 2-D projection. Some papers can show these corresponding conformation. Please help me! - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: [gmx-users] 2D projection and corresponding conformation
Dear sir : I also know these,but can you give some detail procedure for obtaining the corresponding conformations? Thank you in advance! Mark Abraham [EMAIL PROTECTED] 写道： xi zhao wrote: Dear user: We know that observing the sampled conformations in the subspace spanned by the eigenvectors is a so-called two-dimensional projection(2D projection), in 2-D projection, each point represents a snapshot from the simulation, and the distribution shows the sampled region along the first two eigenvectors during the simulation. But I feel confounded, because I do not know to how to obtain corresponding conformation for each point in the 2-D projection. Some papers can show these corresponding conformation. Please help me! Well, if you're after the original 3N-dimensional structure for a given projected point that is known to correspond to an original structure, then you need to arrange for there to be a mapping from original to projected, and then you can apply the reverse mapping. Very likely, once you've constructed the eigenvectors, the code that is plotting these projected points in 2D space will just take the original structures in order and produce the projected points in the same order. Now the reverse mapping is trivial. If you're after a 3N-dimensional structure for an arbitrary point (x1, x2) in projected space which correspond to eigenectors (v1, v2) in 3N-dimensional space, then you need to construct it from the eigenvectors yourself, as x1*v1 + x2*v2. This structure won't be physically realistic, however. The whole point of the eigendecomposition is that any of the structures used as input can be constructed from a linear combination of the eigenvectors. Hopefully, most of the variation is in the first few eigenvectors so that one can approximate the higher-dimensional space by a linear combination of a few eigenvectors - and the weights in the linear combination are members of a low-dimensional space. If this makes no sense, then reading a few chapters of a linear algebra textbook might be in order. :-) Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: [gmx-users] how to remd ana lysi?
I performed remd using GROMACS 3.3.1 at four different temperatures: 270k, 400k, 540k, 660k, and produced four trajectories. I want to know whether my simulation is ok, but I do not know how to analysis my trajectories. Though I have demux.pl script and produced replica_index.xvg and replica_temp.xvg files, the contents of two files are the same! I use trjcat_d to produce a continuous trajectory,according to wiki gromacs. In fact, for a REMD simulation, I can not judge whether the simulations is ok , and if they are ok, how to further analyze or extract useful information from trajectories! Are you clear? Thank you for your help! Mark Abraham [EMAIL PROTECTED] 写道： xi zhao wrote: Dear all users: I performed remd using GROMACS 3.3.1,but I find that I do not know how to analyze the result further, Analyze really doesn't tell us what you're trying to do. though I have demux.pl script and produced replica_index.xvg and replica_temp.xvg files, the contents of two files are the same! I use trjcat_d to produce a continuous trajectory,when analyzing the trajectory, the system shows segment fault? Please give me some advice and analysis tools! You need to tell us what you're trying to do explicitly. That means text describing your intentions, a command line that you tried to use, the output from it, and (potentially) why you think it wasn't what you expected. A segmentation fault is a generic problem with referencing an illegal memory location, and thus just about anything could cause it. If there's no GROMACS-specific error message, though, then it's very likely to be something you've done wrongly. Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to remd analysi?
Dear all users: I performed remd using GROMACS 3.3.1,but I find that I do not know how to analyze the result further,though I have demux.pl script and produced replica_index.xvg and replica_temp.xvg files, the contents of two files are the same! I use trjcat_d to produce a continuous trajectory,when analyzing the trajectory, the system shows segment fault? Please give me some advice and analysis tools! Thank you very much! - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: 回复： Re: 回 复： Re: 回复： Re: 回复 � Re: [gmx-users] about using amb2gmx.pl
Dear sirs: Thank you for your advices! The problem has been wiped off ! David Mobley [EMAIL PROTECTED] 写道： I think I can probably shed a little bit of light here, although Mark is getting close in the last chapter of his e-mail. Basically, pdb2gmx works well for parameterizing proteins, which the chromophore in question isn't, I'm sure. Since we do lots of protein-ligand simulations, where the ligand is not well-handled by pdb2gmx, and since we like the GAFF (Amber) small molecule force field, we have this amb2gmx.pl script which works well for setting up small molecules in AMBER and then converting them to get gromacs .top and .gro files. Xi, what you need to do is something like this: 1) Generate a .top and .gro of your protein only using pdb2gmx. 2) Generate a .top and .gro of your ligand (chromophore) using amb2gmx.pl 3) Generate a combined .top and .gro by: a) For the .top: Turning your ligand .top into a .itp file, as Mark mentions, and including it in the protein topology file. You'll have to see the manual to figure out differences between a .top and a .itp b) For the .gro: There are several options here; you'll have to decide between them by reading the manual or your own preferences. You can either (i) manually (or using a script) generate one by combining the ligand and protein .gro files; (ii) instead of a .gro, use a pdb file (with all hydrogens, in the appropriate order) rather than a gro file as input for grompp or the other gromacs tools. There may be other ways as well. Anyway, where you are at present is apparently step (3). Hope that helps. David 2008/2/17 Mark Abraham : xi zhao wrote: Dear sir: Is my english weak? Not particularly, but it isn't helping you describe clearly :-) I want to simulate pdb:1O5P (www.rcsb.org ), I use amber force field parms in the gromacs. Under this condition, pdb2gmx can not produce chromophore top in the pdb, Why not? You need to tell us why it doesn't work! so I use antechamber and amb2gmx.pl to produce chromophore gro and top files accoding to ffamber website. I do not know how to produce gro and top of entire system. Search the GROMACS wiki for topology file and read chapter 5 of the GROMACS manual to work out how to turn your chromophore .top into an .itp file suitable to include in a GROMACS .top file. Then use whatever technique works for you to do the same with your structure file *without the chromophore* (e.g. pdb2gmx, or via leap and amb2gmx.pl). Then #include your chromophore .itp in that .top file, and give your protein+chromophore structure file and that last .top file to grompp. You will need a detailed knowledge of chapter 5 of the manual, and there's useful information on the wiki too, so read them! Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: 回复： Re: [gmx-use rs] about using amb2gmx.pl
Dear sir : In fact, I have a complex structure(which contains protein and chromophore), though I have known the usual procedure dealing with ligand or drug in the gromacs, such as Prodrg server. Now I want to use Amber force field, and must deal with chromophore molecule in the complex using amb2gmx.pl, then have chromophore.gro and top file. But when the simulation runs, I need a complex entire gro and top files in order to run, but I do not know how to use existing top and gro files to produce entire gro and top . Are you clear? Regards! Mark Abraham [EMAIL PROTECTED] 写道： xi zhao wrote: Dear sir : Can you tell me a detail of procedure, I have only chromophore molecular top,but I need entire top and gro for pdb + chromophore! Your use of terminology is unclear - and you can't afford this sort of lack of clarity in science. pdb, gro and top are all generic file formats. Your first email implied that you did have a file with your initial coordinates. The above implies the opposite. If you lack a file containing your initial coordinates, then you may need to do some serious leg-work to get one, e.g. search the Protein Data Bank. I'd also suggest you follow Justin's advice, and do some tutorial material. If nothing else they should teach you by example some better ways of describing these things! :) Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: 回复： Re: 回 复： Re: [gmx-users] about using amb2gmx.pl
Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding gro top files, but I can only produce chromophore gro and top file using amb2gmx.pl .Are you clear ? Mark Abraham [EMAIL PROTECTED] 写道： xi zhao wrote: Dear sir : In fact, I have a complex structure(which contains protein and chromophore), though I have known the usual procedure dealing with ligand or drug in the gromacs, such as Prodrg server. Now I want to use Amber force field, and must deal with chromophore molecule in the complex using amb2gmx.pl, then have chromophore.gro and top file. But when the simulation runs, I need a complex entire gro and top files in order to run, but I do not know how to use existing top and gro files to produce entire gro and top . Are you clear? If you lack a file containing your initial coordinates, then you may need to do some serious leg-work to get one, e.g. search the Protein Data Bank. It sounds like my earlier advice is appropriate. If you need to insert your chromophore into your protein to form a complex to give yourself an initial structure, then you will need to choose that protein structure in a suitable conformation (this is not trivial) and then to dock that chromophore. How easy it is to do the latter will depend on your available experimental information. Google (or scientific literature) searching for docking and model building is your best bet here - it's well outside the scope of the GROMACS tool set. Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: 回复： Re: 回 复： Re: 回复： Re: [gmx-users] ab out using amb2gmx.pl
Dear sir: Is my english weak? I want to simulate pdb:1O5P (www.rcsb.org), I use amber force field parms in the gromacs. Under this condition, pdb2gmx can not produce chromophore top in the pdb,so I use antechamber and amb2gmx.pl to produce chromophore gro and top files accoding to ffamber website. I do not know how to produce gro and top of entire system. Mark Abraham [EMAIL PROTECTED] 写道： xi zhao wrote: Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding gro top files, but I can only produce chromophore gro and top file using amb2gmx.pl .Are you clear ? No. If you have a structure file already, then you need to read what I wrote earlier. If you don't have a structure file already, then you need to read what I wrote earlier. If you have some problem getting an existing AMBER structure+prmtop to convert properly, then you haven't communicated that. If you haven't got an AMBER structure+prmtop, then give up on amb2gmx.pl Try explaining your problem in English to a friend who doesn't fully understand the science. Then apply the lessons you learned there to describing the problem here :-) Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: 回复： Re: 回 复： Re: 回复： Re: 回复 � Re: [gmx-users] about using amb2gmx.pl
Dear sir : In fact, PRODRG can not produce chromophore top files properly, so I have to give up gromos force field! The normal force field does not have params about chromophore. Justin A. Lemkul [EMAIL PROTECTED] 写道： Search for John Kerrigan's enzyme-ligand tutorial. It explains in clear detail everything you will need to do. Ignore the part about using PRODRG for your chromophore, as you apparently already have this information from antechamber. For the future, it would be more clear to post this type of information: 1. What structures (pdb/gro, doesn't really matter) you already have 2. What topologies you have, and how you generated them 3. Specific errors you are having (from pdb2gmx, etc), not simply I cannot get top and gro for the whole complex. It leaves us wondering what you have or haven't tried doing. -Justin Quoting xi zhao : Dear sir: Is my english weak? I want to simulate pdb:1O5P (www.rcsb.org), I use amber force field parms in the gromacs. Under this condition, pdb2gmx can not produce chromophore top in the pdb,so I use antechamber and amb2gmx.pl to produce chromophore gro and top files accoding to ffamber website. I do not know how to produce gro and top of entire system. Mark Abraham 写道： xi zhao wrote: Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding gro top files, but I can only produce chromophore gro and top file using amb2gmx.pl .Are you clear ? No. If you have a structure file already, then you need to read what I wrote earlier. If you don't have a structure file already, then you need to read what I wrote earlier. If you have some problem getting an existing AMBER structure+prmtop to convert properly, then you haven't communicated that. If you haven't got an AMBER structure+prmtop, then give up on amb2gmx.pl Try explaining your problem in English to a friend who doesn't fully understand the science. Then apply the lessons you learned there to describing the problem here :-) Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about using amb2gmx.pl
Dear all users: I want to simulate a system ( protein + chromophore). I have had chromophore.gro and its top file using amb2gmx.pl,but I find I can not use them to translate PDB( protein + chromophore) file into gro and top files properly. So I need your advice about further procedure! Thank you very much - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: [gmx-users] about using amb2g mx.pl
Dear sir : Can you tell me a detail of procedure, I have only chromophore molecular top,but I need entire top and gro for pdb + chromophore! Mark Abraham [EMAIL PROTECTED] 写道： xi zhao wrote: Dear all users: I want to simulate a system ( protein + chromophore). I have had chromophore.gro and its top file using amb2gmx.pl,but I find I can not use them to translate PDB( protein + chromophore) file into gro and top files properly. So I need your advice about further procedure! Thank you very much You don't need a .gro file. See http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file The grompp utility will happily make a .tpr from your .mdp, your .top file, and your well-formed .pdb file whose atom, residue and molecule names and ordering matches the .top file. This last constraint also applies to a .gro file! Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] demux.pl
Dear all Gromacs users: I want to obtain demux.pl for analysis REMD, but I do not know how to get it, please help me! Thank you very much! - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: [gmx-users] demux.pl
Sorry, but in source of v3.3.2 and 3.3.1 of the website , there is not demux.pl script, please help me! Mark Abraham [EMAIL PROTECTED] 写道： xi zhao wrote: Dear all Gromacs users: I want to obtain demux.pl for analysis REMD, but I do not know how to get it, please help me! Thank you very much! As David van der Spoel said here just today http://www.gromacs.org/pipermail/gmx-users/2008-January/031570.html, and as is noted on the GROMACS wiki http://wiki.gromacs.org/index.php/REMD#Post-processing it's in the source distribution. You'll need to get a source distribution of GROMACS, and to look in the subdirectory referred to in those URLs. Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_energy has no bond entry when MD analysis
Dear friends: when my MD was finished and I want to analyse the bond energy of the protein ,but g_energy did not show bond entry: the first entry is angle? When energy miniumzation finished,g_energy did show G96 bond. why? Please help me! Thank you! - 雅虎邮箱，终生伙伴！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: [gmx-users] g_energy has no bond entry when MD analysis
Yes, I use bond constraints! Mark Abraham [EMAIL PROTECTED] 写道： Dear friends: when my MD was finished and I want to analyse the bond energy of the protein ,but g_energy did not show bond entry: the first entry is angle? When energy miniumzation finished,g_energy did show G96 bond. why? So, when did you use bond length constraints? What effect would they have? Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎邮箱，终生伙伴！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] entropy calaculted script??
Dear Gro-usr friends: I want to calculat the entropy during the md,but lack calculting script for the entropy. Who can provide it for me? Thank you very much! - @yahoo.cn 新域名、无限量，快来抢注！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] phosphated residue???
Dear all There is a phosphate ser in my protein, so when pdb2gmx, the fatal error is atom p is not found How to deal with this problem? how to add the topology file of phosphate ion to residue database? Thank you! - 雅虎免费邮箱3.5G容量，20M附件！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： [gmx-users] about PMF calculation
try mdrun_d and g_wham: Can you tell me how to produce pdo file? thank you very much! 黄永棋 [EMAIL PROTECTED] 写道： Hi gmx-users I am a gromacs beginner, I want to do the PMF calculation ,I have done as the manual said ,I added the ppa, ndx files and got a pdo file . But I don't know what to do with this pdo file. Can anyone tell me what should I do if I want to calculate the PMF? Thanks in advance. Yongqi Huang -- 黄永棋 --- 猜大小单双 16种赚钱的好方法，狂猜狂赚( http://ad4.sina.com.cn/sina/limeng3/mail_zhuiyu/2007/mail_zhuiyu_20070315.html ) === 注册新浪2G免费邮箱（ http://mail.sina.com.cn/chooseMode.html ）___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Mp3疯狂搜-新歌热歌高速下 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: [gmx-users] PMF calculation
Dear Mr Mark Abraham: Can you tell us the details of performing PMF procedures? Thank you very much! Best wish for you! Mark Abraham [EMAIL PROTECTED] 写道： Dear all, I am working on a tripeptide and would like to calculate Potential Mean Force for the tripeptide. Suggestions to calculate PMF are awaited. How about looking for PMF in the manual and reading what it has to say there? Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - 雅虎免费邮箱-3.5G容量，20M附件___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: [gmx-users] r.m.s.i.p
Based on the essential dynamics analysis, the similar of the internal fluctuations in may simulation systems was evaluated by comparing principal subspace first 10 eigenvectors) of each structural trajectory by using the root mean square inner product(RMSIP). Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. Berendsen, H. J. A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292.Mark Abraham [EMAIL PROTECTED] 写道： xi zhao wrote: Dear Gromacs users: I am a new gromacs user, I want ro calculate r.m.s.i.p for exploring similar in motions of two different proteins, I need a script or tools to calculate it. I need your help!I don't know what r.m.s.i.p is. If you want to get help, please definecarefully what you are trying to do - even a link to a journal articlemight work. Please read carefully the gromacs manual section thatdescribes what the utility programs do, in case one of them does it.Mark___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php Mp3疯狂搜-新歌热歌高速下 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: [gmx-users] r.m.s.i.p
Based on the essential dynamics analysis, the similar of the internal fluctuations in may simulation systems was evaluated by comparing principal subspace first 10 eigenvectors) of each structural trajectory by using the root mean square inner product(RMSIP). Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. Berendsen, H. J. A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292.Mark Abraham [EMAIL PROTECTED] 写道： xi zhao wrote: Dear Gromacs users: I am a new gromacs user, I want ro calculate r.m.s.i.p for exploring similar in motions of two different proteins, I need a script or tools to calculate it. I need your help!I don't know what r.m.s.i.p is. If you want to get help, please definecarefully what you are trying to do - even a link to a journal articlemight work. Please read carefully the gromacs manual section thatdescribes what the utility programs do, in case one of them does it.Mark___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php 雅虎免费邮箱-3.5G容量，20M附件___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： RE: [gmx-users] r.m.s.i.p
how to use it in detail?Thanks!"Fan, Fenghui " [EMAIL PROTECTED] 写道： Try RMSD fit function.-Original Message-From: [EMAIL PROTECTED] on behalf of xi zhaoSent: Mon 9/18/2006 2:12 AMTo: gmx-users@gromacs.orgSubject: [gmx-users] r.m.s.i.pDear Gromacs users:I am a new gromacs user, I want ro calculate r.m.s.i.pfor exploring similar in motions of two differentproteins, I need a script or tools to calculate it. Ineed your help!Thank you in advance!Best regard! ___ Mp3???-???http://music.yahoo.com.cn/?source=mail_mailbox_footer___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php 抢注雅虎免费邮箱-3.5G容量，20M附件！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: 回复： Re: [gmx-use rs] r.m.s.i.p
Dear Tsjerk : Thank you very much!Tsjerk Wassenaar [EMAIL PROTECTED] 写道： Hi Xi Zhao,Please find attached a .csh script you can use to calculate the rmsip.The script is of the hand of Isabella Daidone, now in Heidelberg.Note that for a set of 'equal' simulations there is a spread in thevalues you obtain for the RMSIP (i.e. it's not an absolute measure ofequality unless you have full convergence of your simulations). If youwant to use the RMSIP to really compare simulations check our paper inJCC 27 p. 316 (2006).Cheers,TsjerkOn 9/18/06, xi zhao <[EMAIL PROTECTED]>wrote: Based on the essential dynamics analysis, the similar of the internal fluctuations in may simulation systems was evaluated by comparing principal subspace first 10 eigenvectors) of each structural trajectory by using the root mean square inner product(RMSIP). Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. Berendsen, H. J. A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292. Mark Abraham <[EMAIL PROTECTED]>写道： xi zhao wrote: Dear Gromacs users: I am a new gromacs user, I want ro calculate r.m.s.i.p for exploring similar in motions of two different proteins, I need a script or tools to calculate it. I need your help! I don't know what r.m.s.i.p is. If you want to get help, please define carefully what you are trying to do - even a link to a journal article might work. Please read carefully the gromacs manual section that describes what the utility programs do, in case one of them does it. Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php 雅虎免费邮箱-3.5G容量，20M附件 ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Tsjerk A. Wassenaar, Ph.D.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of GroningenNijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php Mp3疯狂搜-新歌热歌高速下 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: 回复： Re: [gmx-use rs] r.m.s.i.p
Thank you for your advise!raja [EMAIL PROTECTED] 写道： HI Zhao,To compute RMSIP, you have to compute eigenvector using gromacs utilityprogram then from that trajectory you can compute RMSIP using a scriptwhich I got from Tsjerk Wassenaar from this list. You can appraoch him.Regards,B.NatarajOn Mon, 18 Sep 2006 16:15:43 +0800 (CST), "xi zhao"<[EMAIL PROTECTED]>said: Based on the essential dynamics analysis, the similar of the internal fluctuations in may simulation systems was evaluated by comparing principal subspace first 10 eigenvectors) of each structural trajectory by using the root mean square inner product(RMSIP). Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. Berendsen, H. J. A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292. Mark Abraham <[EMAIL PROTECTED]>写道： xi zhao wrote: Dear Gromacs users: I am a new gromacs user, I want ro calculate r.m.s.i.p for exploring similar in motions of two different proteins, I need a script or tools to calculate it. I need your help! I don't know what r.m.s.i.p is. If you want to get help, please define carefully what you are trying to do - even a link to a journal article might work. Please read carefully the gromacs manual section that describes what the utility programs do, in case one of them does it. Mark ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php- 雅虎免费邮箱-3.5G容量，20M附件-- raja[EMAIL PROTECTED]-- http://www.fastmail.fm - I mean, what is it about a decent email service?___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php 抢注雅虎免费邮箱-3.5G容量，20M附件！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: [gmx-users] Pobability of con formational distributions!
Dear sir: I can not konwhow to use g_sham combining with PCA? can you give me a example? Thank you very much!David van der Spoel [EMAIL PROTECTED] 写道： xi zhao wrote: Dear sirs: How to calculate the probability of conformational distributions in gromacs by PCA method? I often meet it, but I do not know how to define it! The free energy = -KBTln(probability of conformational distribution).g_sham Thank you for your reply! Mp3疯狂搜-新歌热歌高速下 ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: 46 18 471 4205 fax: 46 18 511 755[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php 抢注雅虎免费邮箱-3.5G容量，20M附件！ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
回复： Re: [gmx-users] Is 2D projection
Dear sir : Can I understand" 2D projection = Component (PC) Probability Distributions P(v1,v2)"? If this is atrue, and howto definethe Pmax in detail? Thankyouin advance!Nguyen Hoang Phuong [EMAIL PROTECTED] 写道： Dear gmx users, Does the 2D projection plot has something to do with convergence of the trajectory? If so, what kind of shape of plot shows the trajectory is non-converged? Normally, I use RMSD plot to see if the trajectory tends to converge. Now my concern is how to see whether trajectory is conserved or not based on 2D projection analyses. Thanks in advance, Lindayou can, for example, have a look at the 2D projection of the trajectory onto the first two principal components obtained from the principal component analysis. In this paper Proteins 2005; 60:485 we used this kind of map to check the convergence of the simulation obtained from a replica exchange simulation with the counterpart obtained from high temperature, normal simulation.Phuong___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php 雅虎免费邮箱-3.5G容量，20M附件___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
