Re: [gmx-users] errores during compilation of GROMACS 3.3.2
Itamar Kass wrote: Dear all, I am trying to compile GROMOCS 3.3.2 on Altix 3700 BX2 (Itanium2 1.6GHz). I am doing something like: On the same machine, I presume (ac.apac.edu.au), using modules fftw/2.1.5-intel-9.1 scsl/1.6.0.0 intel-cc/9.1.051 and ./configure --enable-shared --program-suffix=_3.3.2_double --disable-float --with-fft=fftw2 --with-external-blas --with-external-lapack LIBS="-L/opt/fftw-2.1.5/intel-9.1/lib -lscs" I can reproduce Itamar's problem - which is actually with nb_kernel030_ia64_double, not nb_kernel010_ia64_double as it first appears from his post, probably thanks to his use of "make -j 2". That machine compiles single-precision 3.3.1 as above with no problems, and -scs is the SGI library for LAPACK and BLAS. Removing --disable-float, icc -DHAVE_CONFIG_H -I. -I../../../../src -I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single -I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 -w -MT nb_kernel010_ia64_single.lo -MD -MP -MF .deps/nb_kernel010_ia64_single.Tpo -c ../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single/nb_kernel010_ia64_single.S -fPIC -DPIC -o .libs/nb_kernel010_ia64_single.o compiles with no warnings or errors, but for nb_kernel030_ia64_single... icc -DHAVE_CONFIG_H -I. -I../../../../src -I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single -I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 -w -MT nb_kernel030_ia64_single.lo -MD -MP -MF .deps/nb_kernel030_ia64_single.Tpo -c ../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single/nb_kernel030_ia64_single.S -fPIC -DPIC -o .libs/nb_kernel030_ia64_single.o /tmp/iccJuhOaN.s(1) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(2) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(3) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(4) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(5) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(6) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(7) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(8) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(10) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(15) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(193) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(195) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(269) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(423) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccJuhOaN.s(506) : error A2040: Unexpected token: Unary Diez Operator at: Start .libs/nb_kernel010_ia64_single.o - 15 error(s), 0 warning(s) make[5]: *** [nb_kernel010_ia64_single.lo] Error 1 make[5]: *** Waiting for unfinished jobs /tmp/icc5IXC2M.s(1) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(2) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(3) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(4) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(5) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(6) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(7) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(8) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(10) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(15) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(207) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(261) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(276) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(496) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/icc5IXC2M.s(578) : error A2040: Unexpected token: Unary Diez Operator at: Start .libs/nb_kernel030_ia64_single.o - 15 error(s), 0 warning(s) m With modules gcc/3.3.6 and fftw2/gcc-3.3.3, single precision compiles the non-bonded loops with no problem, although I didn't complete the make, or try double-precision. Itamar, I suggest you try this for yourself, and then ask the APAC admins to install this for you, using the suggestions I make above, rather than use your own /home file space. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search
[gmx-users] errores during compilation of GROMACS 3.3.2
Dear all, I am trying to compile GROMOCS 3.3.2 on Altix 3700 BX2 (Itanium2 1.6GHz). I am doing something like: > ./configure --prefix=/home/564/ixk564/software/gromacs --enable-shared --program-suffix=_3.3.2_double --disable-float --with-fft=fftw2 > make -j 2 and get in replay: icc -DHAVE_CONFIG_H -I. -I../../../../src -I../../../../include -DGMXLIBDIR=\"/home/564/ixk564/software/gromacs/share/top\" -I/opt/fftw-2.1.5/intel-8.1/include -O3 -tpp2 -ip -ftz -MT nb_kernel010_ia64_double.lo -MD -MP -MF .deps/nb_kernel010_ia64_double.Tpo -c nb_kernel010_ia64_double.S -o nb_kernel010_ia64_double.o :3:1: warning: "__PTRDIFF_TYPE__" redefined :4:1: warning: this is the location of the previous definition :4:1: warning: "__SIZE_TYPE__" redefined :3:1: warning: this is the location of the previous definition :3:1: warning: "__PTRDIFF_TYPE__" redefined :4:1: warning: this is the location of the previous definition :4:1: warning: "__SIZE_TYPE__" redefined :3:1: warning: this is the location of the previous definition /tmp/iccK7NleRs(/tmp/iccr4uV6Zs(1) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(2) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(3) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(4) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(5) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(6) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(7) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(8) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(10) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(15) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(211) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(265) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(280) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(520) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccr4uV6Zs(602) : error A2040: Unexpected token: Unary Diez Operator at: Start nb_kernel030_ia64_double.o - 15 error(s), 0 warning(s) 1) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(2) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(3) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(4) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(5) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(6) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(7) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(8) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(10) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(15) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(194) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(196) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(270) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(433) : error A2040: Unexpected token: Unary Diez Operator at: Start /tmp/iccK7NleRs(516) : error A2040: Unexpected token: Unary Diez Operator at: Start nb_kernel010_ia64_double.o - 15 error(s), 0 warning(s) make[5]: *** [nb_kernel030_ia64_double.lo] Error 1 make[5]: *** Waiting for unfinished jobs make[5]: *** [nb_kernel010_ia64_double.lo] Error 1 make[5]: Leaving directory `/home/564/ixk564/software/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel_ia64_double' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/home/564/ixk564/software/gromacs-3.3.2/src/gmxlib/nonbonded' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/564/ixk564/software/gromacs-3.3.2/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/564/ixk564/software/gromacs-3.3.2/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/564/ixk564/software/gromacs-3.3.2/src' make: *** [all-recursive] Error 1 Do you have any idea how to overcome it? Best wishes, Itamar. -- "Prediction is very difficult, especially about the future" - Niels Bohr === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Molecular Dynamics Group | School of Molecular and Microbial Sciences (SMMS) | Chemistry Building (#68) | The University of Queensland | St. Lucia Campus, Brisbane, QLD 4067 | Australia | | Tel: +61 7 3365 9922 | Fax: +61 7 3365 3872 | E-mail: [EMAIL PROTECTED] | Web page: http://compbio.chemistry.uq.edu.au/md/ikass/
Re: [gmx-users] the comm_mode
Hi, It's about geometry. Be pragmatic. By inspecting the trajectory, you can which one works. if Linear works for your system, use it; otherwise, use rotation. Although I prefer to use Rotation for simulations in vacuum in the first place, and for first few ns simulation for big protein with explicit solvent. Regards, Yang Ye On 10/15/2007 12:24 AM, OZGE ENGIN wrote: Sorry, but I have to ask some more questions. I have just started to perform simulations in vacuum. I can understand not using of PME in vacuum simulations; however, I can not understand the sentence you wrote : 'rotation is recomended.' COM velocity removal's effect is directly visible. Is it related to conservation of angular momentum? Thank you very much! Oz. -Original Message- From: Yang Ye <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Sun, 14 Oct 2007 07:07:18 -0700 (PDT) Subject: Re: Re: [gmx-users] the comm_mode - Original Message From: OZGE ENGIN <[EMAIL PROTECTED]> To: [EMAIL PROTECTED]; gmx-users@gromacs.org Cc: gmx-users@gromacs.org Sent: Sunday, October 14, 2007 8:33:28 PM Subject: Re: Re: [gmx-users] the comm_mode Hi Yang, I am performing a simulation of a peptide in vacuum, and in the mailing archieve, I read that using of linear option of comm_mode in the vacuum simulations. Is it due to the relatively rapid convergence of molecules in the vacuum environment? It is not because of this reason, it is due to PBC. Simulation in vacuum is usually done without PBC, Rotation is recommended. COM velocity removal's effect is directly visible, so if "Linear" works for you, you may use it. Thanks in advance Ozge -Original Message- From: Yang Ye <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Sun, 14 Oct 2007 03:42:12 -0700 (PDT) Subject: Re: [gmx-users] the comm_mode Generally, linear. For simulation in vacumm, you need rotation. With big molecules, equilibration may not be done thoroughly; this may result in very obivious rotation that Linear can not prevent. So visualize your trajectory and check your molecule. If it happens, you need to apply Rotation in the beginning of your simulation for a few ns. Regards, Yang Ye - Original Message From: Dechang Li <[EMAIL PROTECTED]> To: gmx-users Sent: Sunday, October 14, 2007 5:34:35 PM Subject: [gmx-users] the comm_mode Dear all, There are three options of comm_mode: Linear, Angular and none. The option Angular is said that "Remove center of mass translation and rotation around the center of mass". Does it mean the option Angular remove the translation and rotation BOTH ? If I want to do a simulation such as a protein in the explicit water, which option would be better? Or it will be the same? Thank you for your reply. Best regards, 2007-10-14 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Tool for visualizing disulphide bonds
Hi, On Oct 13, 2007, at 6:12 PM, Yang Ye wrote: Program like VMD can draw extra bond. You need to get its manual and code a line or two in TCL. Regards, Yang Ye On 10/14/2007 11:38 PM, van Bemmelen wrote: Hi Ozge, I'm not sure what you mean by "visualization". But what about using VMD for trajectory visualization and creating a representation that contains only the sulphur atoms forming the disulphide bonds? The big caveat with disulphides is of course that they are covalent bonds, and therefore assigned in the topology (pdb2gmx uses input structure distances to determine whether to connect them). Even if the molecule would like to move apart and break them, they will be intact for the entire simulation since we put them there. Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ngmx error messages
Hi, On Oct 13, 2007, at 6:04 PM, Sagittarius wrote: I already have some kind of cygwin. Could you please provide me with more details on "install cygwin with some kind of X server" Thank you in advance Actually, if you don't absolutely need ngmx you can just disable the X11-dependent parts with the configure flag --without-x. Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: Re: [gmx-users] the comm_mode
Sorry, but I have to ask some more questions. I have just started to perform simulations in vacuum. I can understand not using of PME in vacuum simulations; however, I can not understand the sentence you wrote : 'rotation is recomended.' COM velocity removal's effect is directly visible. Is it related to conservation of angular momentum? Thank you very much! Oz. -Original Message- From: Yang Ye <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Date: Sun, 14 Oct 2007 07:07:18 -0700 (PDT) Subject: Re: Re: [gmx-users] the comm_mode - Original Message From: OZGE ENGIN <[EMAIL PROTECTED]> To: [EMAIL PROTECTED]; gmx-users@gromacs.org Cc: gmx-users@gromacs.org Sent: Sunday, October 14, 2007 8:33:28 PM Subject: Re: Re: [gmx-users] the comm_mode Hi Yang, I am performing a simulation of a peptide in vacuum, and in the mailing archieve, I read that using of linear option of comm_mode in the vacuum simulations. Is it due to the relatively rapid convergence of molecules in the vacuum environment? >> It is not because of this reason, it is due to PBC. Simulation in vacuum is >> usually done without PBC, Rotation is recommended. >> COM velocity removal's effect is directly visible, so if "Linear" works for >> you, you may use it. Thanks in advance Ozge -Original Message- From: Yang Ye <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Sun, 14 Oct 2007 03:42:12 -0700 (PDT) Subject: Re: [gmx-users] the comm_mode Generally, linear. For simulation in vacumm, you need rotation. With big molecules, equilibration may not be done thoroughly; this may result in very obivious rotation that Linear can not prevent. So visualize your trajectory and check your molecule. If it happens, you need to apply Rotation in the beginning of your simulation for a few ns. Regards, Yang Ye - Original Message From: Dechang Li <[EMAIL PROTECTED]> To: gmx-users Sent: Sunday, October 14, 2007 5:34:35 PM Subject: [gmx-users] the comm_mode Dear all, There are three options of comm_mode: Linear, Angular and none. The option Angular is said that "Remove center of mass translation and rotation around the center of mass". Does it mean the option Angular remove the translation and rotation BOTH ? If I want to do a simulation such as a protein in the explicit water, which option would be better? Or it will be the same? Thank you for your reply. Best regards, 2007-10-14 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Tool for visualizing disulphide bonds
Program like VMD can draw extra bond. You need to get its manual and code a line or two in TCL. Regards, Yang Ye On 10/14/2007 11:38 PM, van Bemmelen wrote: Hi Ozge, I'm not sure what you mean by "visualization". But what about using VMD for trajectory visualization and creating a representation that contains only the sulphur atoms forming the disulphide bonds? If that doesn't answer your question, please be more specific. Cheers, Jeroen Date: Sun, 14 Oct 2007 15:45:24 +0300 From: "OZGE ENGIN" <[EMAIL PROTECTED]> Subject: [gmx-users] Tool for visualizing disulphide bonds To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="UTF-8" Hi all, Is there any tool for the visualization of disulphide bonds along the whole trajectory? Regards, Ozge ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Tool for visualizing disulphide bonds
Hi Ozge, I'm not sure what you mean by "visualization". But what about using VMD for trajectory visualization and creating a representation that contains only the sulphur atoms forming the disulphide bonds? If that doesn't answer your question, please be more specific. Cheers, Jeroen >Date: Sun, 14 Oct 2007 15:45:24 +0300 >From: "OZGE ENGIN" <[EMAIL PROTECTED]> >Subject: [gmx-users] Tool for visualizing disulphide bonds >To: gmx-users@gromacs.org >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="UTF-8" > >Hi all, > >Is there any tool for the visualization of disulphide bonds >along the whole trajectory? > >Regards, > >Ozge ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] the comm_mode
- Original Message From: OZGE ENGIN <[EMAIL PROTECTED]> To: [EMAIL PROTECTED]; gmx-users@gromacs.org Cc: gmx-users@gromacs.org Sent: Sunday, October 14, 2007 8:33:28 PM Subject: Re: Re: [gmx-users] the comm_mode Hi Yang, I am performing a simulation of a peptide in vacuum, and in the mailing archieve, I read that using of linear option of comm_mode in the vacuum simulations. Is it due to the relatively rapid convergence of molecules in the vacuum environment? >> It is not because of this reason, it is due to PBC. Simulation in vacuum is >> usually done without PBC, Rotation is recommended. >> COM velocity removal's effect is directly visible, so if "Linear" works for >> you, you may use it. Thanks in advance Ozge -Original Message- From: Yang Ye <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Sun, 14 Oct 2007 03:42:12 -0700 (PDT) Subject: Re: [gmx-users] the comm_mode Generally, linear. For simulation in vacumm, you need rotation. With big molecules, equilibration may not be done thoroughly; this may result in very obivious rotation that Linear can not prevent. So visualize your trajectory and check your molecule. If it happens, you need to apply Rotation in the beginning of your simulation for a few ns. Regards, Yang Ye - Original Message From: Dechang Li <[EMAIL PROTECTED]> To: gmx-users Sent: Sunday, October 14, 2007 5:34:35 PM Subject: [gmx-users] the comm_mode Dear all, There are three options of comm_mode: Linear, Angular and none. The option Angular is said that "Remove center of mass translation and rotation around the center of mass". Does it mean the option Angular remove the translation and rotation BOTH ? If I want to do a simulation such as a protein in the explicit water, which option would be better? Or it will be the same? Thank you for your reply. Best regards, 2007-10-14 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] =___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] the comm_mode
Hi Yang, I am performing a simulation of a peptide in vacuum, and in the mailing archieve, I read that using of linear option of comm_mode in the vacuum simulations. Is it due to the relatively rapid convergence of molecules in the vacuum environment? Thanks in advance Ozge -Original Message- From: Yang Ye <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Sun, 14 Oct 2007 03:42:12 -0700 (PDT) Subject: Re: [gmx-users] the comm_mode Generally, linear. For simulation in vacumm, you need rotation. With big molecules, equilibration may not be done thoroughly; this may result in very obivious rotation that Linear can not prevent. So visualize your trajectory and check your molecule. If it happens, you need to apply Rotation in the beginning of your simulation for a few ns. Regards, Yang Ye - Original Message From: Dechang Li <[EMAIL PROTECTED]> To: gmx-users Sent: Sunday, October 14, 2007 5:34:35 PM Subject: [gmx-users] the comm_mode Dear all, There are three options of comm_mode: Linear, Angular and none. The option Angular is said that "Remove center of mass translation and rotation around the center of mass". Does it mean the option Angular remove the translation and rotation BOTH ? If I want to do a simulation such as a protein in the explicit water, which option would be better? Or it will be the same? Thank you for your reply. Best regards, 2007-10-14 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Tool for visualizing disulphide bonds
Hi all, Is there any tool for the visualization of disulphide bonds along the whole trajectory? Regards, Ozge ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Designing a topology file: bonded/non-bonded mess
Frankie Montenegro wrote: Wow, I didn't realize you guys in Europe work 24/7 too. On Sunday morning nonetheless :-) new on the list? (I know you're not...) On 10/14/07, David van der Spoel <[EMAIL PROTECTED]> wrote: question: are there chemical bonds between "molecules" (which you seem to imply by stating the sites are connected by an aromatic ring). If there are then your whole system should be considered as a single molecule. Have you tried x2top on this? (gmx 3.3.2 only). Yes they are. x2top wouldn't work, most atoms are redefined (two types of O with different charges, two types of C, etc. All are custom-fitted with Gaussians and GULP) I don't think treating the whole system as one molecule could work. A single "cell" of the crystall would have over 250 atoms, and I need 2x2 structure minimum, probably even bigger. But that might be last resort (after all , aren't some proteins over couple of thousand atoms?) you can tune x2top as you see fit by editing the ffoplsaa.n2t file. Size is not a problem, and you can use periodic molecules as well. Not sure what you're after, but I hope you realize that GROMACS can only do pair potentials, so no funky non-bonded three body potentials. BTW, what is the slope of GMX_performance vs. molecule_size curve ? There is one more regrouping that I am trying right now (namely having two moleculetypes: "cube-edge" and "cube-node", adding some table "LJ" in between). If this doesn't go, I am out of ideas. Thanks anyway. ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Designing a topology file: bonded/non-bonded mess
Wow, I didn't realize you guys in Europe work 24/7 too. On Sunday morning nonetheless :-) On 10/14/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > question: are there chemical bonds between "molecules" (which you seem > to imply by stating the sites are connected by an aromatic ring). If > there are then your whole system should be considered as a single > molecule. Have you tried x2top on this? (gmx 3.3.2 only). > Yes they are. x2top wouldn't work, most atoms are redefined (two types of O with different charges, two types of C, etc. All are custom-fitted with Gaussians and GULP) I don't think treating the whole system as one molecule could work. A single "cell" of the crystall would have over 250 atoms, and I need 2x2 structure minimum, probably even bigger. But that might be last resort (after all , aren't some proteins over couple of thousand atoms?) BTW, what is the slope of GMX_performance vs. molecule_size curve ? There is one more regrouping that I am trying right now (namely having two moleculetypes: "cube-edge" and "cube-node", adding some table "LJ" in between). If this doesn't go, I am out of ideas. Thanks anyway. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the comm_mode
Generally, linear. For simulation in vacumm, you need rotation. With big molecules, equilibration may not be done thoroughly; this may result in very obivious rotation that Linear can not prevent. So visualize your trajectory and check your molecule. If it happens, you need to apply Rotation in the beginning of your simulation for a few ns. Regards, Yang Ye - Original Message From: Dechang Li <[EMAIL PROTECTED]> To: gmx-users Sent: Sunday, October 14, 2007 5:34:35 PM Subject: [gmx-users] the comm_mode Dear all, There are three options of comm_mode: Linear, Angular and none. The option Angular is said that "Remove center of mass translation and rotation around the center of mass". Does it mean the option Angular remove the translation and rotation BOTH ? If I want to do a simulation such as a protein in the explicit water, which option would be better? Or it will be the same? Thank you for your reply. Best regards, 2007-10-14 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] =___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the comm_mode
Dechang Li wrote: > Dear all, > > There are three options of comm_mode: Linear, Angular and none. > The option Angular is said that "Remove center of mass translation > and rotation around the center of mass". Does it mean the option > Angular remove the translation and rotation BOTH ? yes > If I want to do a simulation such as a protein in the explicit > water, which option would be better? Or it will be the same? > Thank you for your reply. > linear. angular with PBC will give artifacts > -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Designing a topology file: bonded/non-bonded mess
Frankie Montenegro wrote: Hi all, I am hoping someone could give me advice regarding a topology file design. I am trying to implement a forcefield for an organic crystal with 30 atoms at each site (therefore, 30 atom basis). Sites are connected by an aromatic ring. The forcefield I am trying to implement does not treat ring as a single unit; rather, carbons are a part of the 3- and 4- body interactions with other atoms from the site, and two of them have harmonic term between themselves. Initially, I tried to set each (30-atom) site as one "moleculetype". So, half of the aromatic ring would be in one "moleculetype", and half of it in the neighbor. But then I have to set up BONDED interactions between atoms from DIFFERENT molecules. And not just one, three of them: torsion, angle term and multiple harmonic terms. I was hoping someone could see a solution here. I tried regrouping ring carbons to different molecules (sacrifising symmetry) but I always end up with a bonded interaction between "nonbonded" atoms. question: are there chemical bonds between "molecules" (which you seem to imply by stating the sites are connected by an aromatic ring). If there are then your whole system should be considered as a single molecule. Have you tried x2top on this? (gmx 3.3.2 only). Any suggestion is appreciated. F. ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the comm_mode
Dear all, There are three options of comm_mode: Linear, Angular and none. The option Angular is said that "Remove center of mass translation and rotation around the center of mass". Does it mean the option Angular remove the translation and rotation BOTH ? If I want to do a simulation such as a protein in the explicit water, which option would be better? Or it will be the same? Thank you for your reply. Best regards, 2007-10-14 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Designing a topology file: bonded/non-bonded mess
Hi all, I am hoping someone could give me advice regarding a topology file design. I am trying to implement a forcefield for an organic crystal with 30 atoms at each site (therefore, 30 atom basis). Sites are connected by an aromatic ring. The forcefield I am trying to implement does not treat ring as a single unit; rather, carbons are a part of the 3- and 4- body interactions with other atoms from the site, and two of them have harmonic term between themselves. Initially, I tried to set each (30-atom) site as one "moleculetype". So, half of the aromatic ring would be in one "moleculetype", and half of it in the neighbor. But then I have to set up BONDED interactions between atoms from DIFFERENT molecules. And not just one, three of them: torsion, angle term and multiple harmonic terms. I was hoping someone could see a solution here. I tried regrouping ring carbons to different molecules (sacrifising symmetry) but I always end up with a bonded interaction between "nonbonded" atoms. Any suggestion is appreciated. F. ___ 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
