Re: [gmx-users] Coarse-grained force field
Hi Ksenie, I don't think you'll be able to find a proper atomistic force field description for lanthanide either. Check http://www.gromacs.org/Documentation/How-tos/Parameterization. But in general, no, you can't mix force fields, and definitely not ones of different resolution. In addition, think of what it means, a coarse grained ion. Usually it's either something that binds one part of a protein to another (emulate with some bonds), or it is a sphere of water with something in it that happens to bear some charge, like in the ion definitions in Martini. Cheers, Tsjerk On Wed, Apr 20, 2011 at 7:54 AM, ksenia248 ksenia...@gmail.com wrote: Hello. I am trying to simulate the supramolecular organization of liquid crystalline complex of lanthanide by coarse-grained molecular dynamics. But I have some problems with force fields. I can not find coarse-grained force field for lanthanide ion. Can I use atomistic force field oplsaa.ff for lanthanide ion and Martinin force field for other groups of atoms together in one simulation? Or may be you can recommend me some other coarse-grained force fields? Thank you very much. -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
Hi,
Pymol is sort of semi commercial. You can install it easily on Ubuntu,
using apt-get install pymol (free!), you can install from source (also
free!). You can obtain an educational build (also free!, though
requiring registration). Any will do for the building of sequences,
which on linux is as simple as running:
for i in Y W F A; do for j in Y W F A; do for k in Y W F A; do for l
in Y W F A; do
PEP=H$i$j$k$lPAS
pymol -qcd editor.build_peptide('${PEP}');cmd.save('$PEP.pdb')
done; done; done; done
Hope it helps,
Tsjerk
2011/4/20 Terry terrence...@gmail.com:
Hi Chuan,
Leap is a part of Ambertools which is free.
See http://ambermd.org/#AmberTools
Good luck.
Terry
2011/4/20 Liao Chuan liaoch...@tju.edu.cn
HI, Itamer and Mark, thanks for your prompt replies.
Pymol, Amber and Sybyl are commercial software. Any free software/scripts?
- Chuan
发件人: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
代表 Mark Abraham
发送时间: 2011年4月20日 13:31
收件人: Discussion list for GROMACS users
主题: Re: [gmx-users] any software which could convert a polypeptidesequence
to a pdb file?
On 4/20/2011 2:36 PM, Liao Chuan wrote:
Dear gmx-users,
I want to conduct simulations of a protein and its ligand, a heptapeptide
HXXXPAS, where X could be tyrosine, tryptophan, pheny alanine, alanine.
Thus, I will have to conduct a total number of 4*4*4=64 runs. I've got the
pdb file of the protein, but I have no idea how to prepare the pdb files of
those 64 heptapeptides with sequences already known. Is there any
software/script which could convert a polypeptide sequence to a pdb file?
Any comment is appreciated!
Leap in the AmberTools package is good for this.
Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] dhfr-impl-1nm.bench run keeps failing
Hello, I am trying to run the dhfr-impl-1nm.bench benchmark but this keeps failing. I am using Gromacs 4.5.3 built using both Intel and PGI compilers, but both builds fail with the error message: MPI Application rank 1 exited before MPI_Finalize() with status 0 The rank and the status value vary. Any idea what could be wrong? Thanks in advance, -- Wadud Miah, High Performance Computing Systems Developer Research Computing Services, University of East Anglia Web: http://www.uea.ac.uk/~xca10fju/ Telephone: 01603 593856 Information Services -- -- 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] dhfr-impl-1nm.bench run keeps failing
On 4/20/2011 6:57 PM, Miah Wadud Dr (ITCS) wrote: Hello, I am trying to run the dhfr-impl-1nm.bench benchmark but this keeps failing. I am using Gromacs 4.5.3 built using both Intel and PGI compilers, but both builds fail with the error message: MPI Application rank 1 exited before MPI_Finalize() with status 0 The rank and the status value vary. Any idea what could be wrong? No idea. That's just a generic advisory from the MPI library. Only the mdrun stdout or .log file could have a GROMACS-specific diagnostic message. You need to be sure that you can run other MPI programs, too. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4dae452b.3090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new installation. Mark -- Ragothaman M Yennamalli, Ph.D. Postdoctoral Research Associate 1012 Crop Genome Informatics Laboratory Department of Genetics, Development and Cell Biology Iowa State University Ames, Iowa 50011-3260 USA +1 515-294-8971 (Office) +1 515-294-8280 (Fax) +1 515-851-1016 (Mobile) When you can do the common things of life in an uncommon way, you will command the attention of the world. -George Washington Carver http://www.public.iastate.edu/~raghu/ http://www.artistrkrishnarao.com/ *** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
These were the exact commands used to install fftw 3.2.2 ./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared CC=cc F77=f77 make -j 48 make install These were the exact commands used to install gromacs4.5.4 ./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS' make -j 48 make install I had installed the gromacs version 4.5.3 earlier and encountered the same problem with pdb2gmx. Hence installed the latest version. Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Please provide the exact commands that you used to install Gromacs. What exactly were the issues that you had to circumvent? Have you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org mailto: gmx-users@gromacs.org Message-ID: 4dae452b.3090...@anu.edu.au mailto: 4dae452b.3090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new installation. Mark -- Ragothaman M Yennamalli, Ph.D. Postdoctoral Research Associate 1012 Crop Genome Informatics Laboratory Department of Genetics, Development and Cell Biology Iowa State University Ames, Iowa 50011-3260 USA +1 515-294-8971 (Office) +1 515-294-8280 (Fax) +1 515-851-1016 (Mobile) When you can do the common things of life in an uncommon way, you will command the attention of the world. -George Washington Carver http://www.public.iastate.edu/~raghu/ http://www.public.iastate.edu/%7Eraghu/ http://www.artistrkrishnarao.com/ *** -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ragothaman M Yennamalli, Ph.D. Postdoctoral Research Associate 1012 Crop Genome Informatics Laboratory Department of Genetics, Development and Cell Biology Iowa State University Ames, Iowa 50011-3260 USA +1 515-294-8971 (Office) +1 515-294-8280 (Fax) +1 515-851-1016 (Mobile) When you can do the common things of life in an uncommon way, you will command the attention of the world. -George Washington Carver http://www.public.iastate.edu/~raghu/ http://www.artistrkrishnarao.com/ *** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Microporous simulation
Hi everyone I am trying to run a simulation of Alpo (aluminophosphates) microporous material, the topology of the material was build using x2top (it had been checked). I got all the bonding and nonbonding parameters, when I run the energy minimization of this system, Iget this : Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=1 There were 420 inconsistent shifts. Check your topology Step=0, Dmax= 1.0e-02 nm, Epot= 3.25885e+04 Fmax= 0.0e+00, atom= 0 writing lowest energy coordinates. Steepest Descents converged to Fmax 10 in 1 steps Potential Energy = 3.2588531e+04 Maximum force = 0.000e+00 on atom 0 Norm of force = 0.000e+00 gcq#152: I Smell Smoke From a Gun Named Extinction (Pixies) When I look my finally PDB the structure of microporus material, some atoms appear outside the box. I don't know how to fix the atoms inside the box? and avoid this inconsistent shift. who can help me with this? Thanks This message was sent using IMP, the Internet Messaging Program. -- 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] dhfr-impl-1nm.bench run keeps failing
The MPI library is able to run other MPI jobs as well as other parallel Gromacs runs, and it just seems like this run causes this difficulty. I am using Platform MPI 8.1. Regards, Wadud. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Wednesday, April 20, 2011 12:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dhfr-impl-1nm.bench run keeps failing On 4/20/2011 6:57 PM, Miah Wadud Dr (ITCS) wrote: Hello, I am trying to run the dhfr-impl-1nm.bench benchmark but this keeps failing. I am using Gromacs 4.5.3 built using both Intel and PGI compilers, but both builds fail with the error message: MPI Application rank 1 exited before MPI_Finalize() with status 0 The rank and the status value vary. Any idea what could be wrong? No idea. That's just a generic advisory from the MPI library. Only the mdrun stdout or .log file could have a GROMACS-specific diagnostic message. You need to be sure that you can run other MPI programs, too. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
Ragothaman Yennamalli wrote: These were the exact commands used to install fftw 3.2.2 ./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared CC=cc F77=f77 make -j 48 make install These were the exact commands used to install gromacs4.5.4 ./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS' I'm no compiler expert, but is it necessary to set all these CFLAGS here? Does the installation fail for some reason if they're not set? Also, how is Gromacs finding FFTW? You haven't set the CPPFLAGS or LDFLAGS. make -j 48 make install I had installed the gromacs version 4.5.3 earlier and encountered the same problem with pdb2gmx. Hence installed the latest version. This would indicate to me that the problem is not necessarily in Gromacs, but the way you're installing it, and as Mark suggested, is probably related to some static/shared library issue. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Please provide the exact commands that you used to install Gromacs. What exactly were the issues that you had to circumvent? Have you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new installation. Mark -- Ragothaman M Yennamalli, Ph.D. Postdoctoral Research Associate 1012 Crop Genome Informatics Laboratory Department of Genetics, Development and Cell Biology Iowa State University Ames, Iowa 50011-3260 USA +1 515-294-8971 tel:%2B1%20515-294-8971 (Office) +1 515-294-8280 tel:%2B1%20515-294-8280 (Fax) +1 515-851-1016 tel:%2B1%20515-851-1016 (Mobile) When you can do the common things of life in an uncommon way, you will command the attention of the world. -George Washington Carver http://www.public.iastate.edu/~raghu/ http://www.public.iastate.edu/%7Eraghu/ http://www.public.iastate.edu/%7Eraghu/ http://www.artistrkrishnarao.com/ *** -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ragothaman M Yennamalli, Ph.D. Postdoctoral Research Associate 1012 Crop Genome Informatics Laboratory Department of
Re: [gmx-users] Microporous simulation
Hernan Ahumada wrote: Hi everyone I am trying to run a simulation of Alpo (aluminophosphates) microporous material, the topology of the material was build using x2top (it had been checked). I got all the bonding and nonbonding parameters, when I run the energy minimization of this system, Iget this : Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=1 There were 420 inconsistent shifts. Check your topology Step=0, Dmax= 1.0e-02 nm, Epot= 3.25885e+04 Fmax= 0.0e+00, atom= 0 writing lowest energy coordinates. Steepest Descents converged to Fmax 10 in 1 steps Potential Energy = 3.2588531e+04 Maximum force = 0.000e+00 on atom 0 Norm of force = 0.000e+00 gcq#152: I Smell Smoke From a Gun Named Extinction (Pixies) When I look my finally PDB the structure of microporus material, some atoms appear outside the box. I don't know how to fix the atoms inside the box? and avoid this inconsistent shift. who can help me with this? The inconsistent shifts and high potential energy indicate that the system has blown up due to instability. There is no way to simply fix the atoms in the box aside from preparing a system that can actually be energy-minimized. It is odd to me that the force is zero. Which Gromacs version is this? What hardware are you running it on, and how did you install it (exact commands, please)? I ran into this problem a long time ago due to an as-yet unresolved bug, but I am hesitant to suggest that without knowing a whole lot more about your setup. -Justin Thanks This message was sent using IMP, the Internet Messaging Program. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
Dear Justin, Thanks for the mail. Yes, without these CFLAGS the make was not successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring gromacs. Since without it it would have stopped compiling. I want to agree with you that it is some issue with shared libraries, but i dont think it is the issue since I have used the flag --enable-shared. Also, if this was the case then editconf would not have worked as well. Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 8:33 AM, Justin A. Lemkul jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: These were the exact commands used to install fftw 3.2.2 ./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared CC=cc F77=f77 make -j 48 make install These were the exact commands used to install gromacs4.5.4 ./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS' I'm no compiler expert, but is it necessary to set all these CFLAGS here? Does the installation fail for some reason if they're not set? Also, how is Gromacs finding FFTW? You haven't set the CPPFLAGS or LDFLAGS. make -j 48 make install I had installed the gromacs version 4.5.3 earlier and encountered the same problem with pdb2gmx. Hence installed the latest version. This would indicate to me that the problem is not necessarily in Gromacs, but the way you're installing it, and as Mark suggested, is probably related to some static/shared library issue. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Please provide the exact commands that you used to install Gromacs. What exactly were the issues that you had to circumvent? Have you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new installation. Mark -- Ragothaman M Yennamalli, Ph.D. Postdoctoral Research Associate 1012 Crop Genome Informatics Laboratory Department of Genetics, Development and Cell Biology Iowa State University Ames, Iowa 50011-3260 USA +1 515-294-8971 tel:%2B1%20515-294-8971 (Office) +1 515-294-8280 tel:%2B1%20515-294-8280 (Fax) +1 515-851-1016 tel:%2B1%20515-851-1016 (Mobile) When you can do the common things of life in an uncommon way, you will command the attention of the world. -George Washington Carver http://www.public.iastate.edu/~raghu/ http://www.public.iastate.edu/%7Eraghu/ http://www.public.iastate.edu/%7Eraghu/ http://www.artistrkrishnarao.com/ *** -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org
Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
There is another free tool (Avogadro) which is pretty easy to handle this also. Try http://avogadro.openmolecules.net/wiki/Get_Avogadro in Build -- Inert --- Peptides, Which is very easy to use. you can choose Straight line, beta sheet or alpha helix or other. and save as .pdb lina -- 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: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
apt-get install avogadro http://avogadro.openmolecules.net/wiki/Distribution_Packages On Wed, Apr 20, 2011 at 10:34 PM, ZHAO Lina lnzha...@gmail.com wrote: There is another free tool (Avogadro) which is pretty easy to handle this also. Try http://avogadro.openmolecules.net/wiki/Get_Avogadro in Build -- Inert --- Peptides, Which is very easy to use. you can choose Straight line, beta sheet or alpha helix or other. and save as .pdb lina -- 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] pdb2gmx segmentation fault
Ragothaman Yennamalli wrote: Dear Justin, Thanks for the mail. Yes, without these CFLAGS the make was not successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring gromacs. Since without it it would have stopped compiling. I want to agree with you that it is some issue with shared libraries, but i dont think it is the issue since I have used the flag --enable-shared. Also, You did --enable-shared for FFTW, but not Gromacs. Perhaps there is some mismatch there. if this was the case then editconf would not have worked as well. I wouldn't rule it out just yet. If the installation was successful, everything would work. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 8:33 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: These were the exact commands used to install fftw 3.2.2 ./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared CC=cc F77=f77 make -j 48 make install These were the exact commands used to install gromacs4.5.4 ./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS' I'm no compiler expert, but is it necessary to set all these CFLAGS here? Does the installation fail for some reason if they're not set? Also, how is Gromacs finding FFTW? You haven't set the CPPFLAGS or LDFLAGS. make -j 48 make install I had installed the gromacs version 4.5.3 earlier and encountered the same problem with pdb2gmx. Hence installed the latest version. This would indicate to me that the problem is not necessarily in Gromacs, but the way you're installing it, and as Mark suggested, is probably related to some static/shared library issue. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Please provide the exact commands that you used to install Gromacs. What exactly were the issues that you had to circumvent? Have you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new installation. Mark -- Ragothaman M Yennamalli, Ph.D. Postdoctoral Research Associate 1012 Crop Genome Informatics Laboratory Department of
Re: [gmx-users] pdb2gmx segmentation fault
On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: Dear Justin, Thanks for the mail. Yes, without these CFLAGS the make was not successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring gromacs. Since without it it would have stopped compiling. I want to agree with you that it is some issue with shared libraries, but i dont think it is the issue since I have used the flag --enable-shared. Also, You did --enable-shared for FFTW, but not Gromacs. Perhaps there is some mismatch there. Since configure did not have any such option, i did not use it. However, I tried compiling with --enable-shared to reinstall gromacs. It installed without any issues. But, the same segmentation fault. if this was the case then editconf would not have worked as well. I wouldn't rule it out just yet. If the installation was successful, everything would work. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 8:33 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: These were the exact commands used to install fftw 3.2.2 ./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared CC=cc F77=f77 make -j 48 make install These were the exact commands used to install gromacs4.5.4 ./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS' I'm no compiler expert, but is it necessary to set all these CFLAGS here? Does the installation fail for some reason if they're not set? Also, how is Gromacs finding FFTW? You haven't set the CPPFLAGS or LDFLAGS. make -j 48 make install I had installed the gromacs version 4.5.3 earlier and encountered the same problem with pdb2gmx. Hence installed the latest version. This would indicate to me that the problem is not necessarily in Gromacs, but the way you're installing it, and as Mark suggested, is probably related to some static/shared library issue. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Please provide the exact commands that you used to install Gromacs. What exactly were the issues that you had to circumvent? Have you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au mailto:4dae452b.3090...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top Probably, no other GROMACS command works either, because of some shared library issue related to your new
Re: [gmx-users] pdb2gmx segmentation fault
I've never seen the -D_POSIX_PTHREAD_SEMANTICS before. What caused you to need to define that flag? Also...what hardware (cpu) and operating system (linux? what distro? what version?) are you using? Matt Z. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_velacc -mol
I'm a recent gromacs user and right now I'm starting to calculate velocity autocorrelation functions for a pure compound, using g_velacc. I'd like to know something more about the properties and consequences of the option -mol and what exactly the program does if the option is not included. I'm trying to obtain velocity autocorrelation functions for pure water for testing purposes and when the option -mol is included the system returns the message core dumped. Thanks Luis Martins -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_velacc -mol
On 2011-04-20 18.30, Luis Martins wrote: I'm a recent gromacs user and right now I'm starting to calculate velocity autocorrelation functions for a pure compound, using g_velacc. I'd like to know something more about the properties and consequences of the option -mol and what exactly the program does if the option is not included. I'm trying to obtain velocity autocorrelation functions for pure water for testing purposes and when the option -mol is included the system returns the message core dumped. Thanks Luis Martins Even if you have a correct index file? Try g_velacc -h -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] density off
Hello, I am trying to obtain the density for my system that is exactly identical to experimental value but whatever pressure I apply density is still off by 3%. Is this issue common? -- Thanks, Jennifer N. -- 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] density off
On 2011-04-20 19.40, Juliette N. wrote: Hello, I am trying to obtain the density for my system that is exactly identical to experimental value but whatever pressure I apply density is still off by 3%. Is this issue common? -- Thanks, Jennifer N. Yes, force fields are not perfect. How about running NVT at the experimental density and measuring the pressure? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] density off
Hi David, I used to apply NPT to fix the density, how can I get the denisty using NVT? On 20 April 2011 13:46, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-04-20 19.40, Juliette N. wrote: Hello, I am trying to obtain the density for my system that is exactly identical to experimental value but whatever pressure I apply density is still off by 3%. Is this issue common? -- Thanks, Jennifer N. Yes, force fields are not perfect. How about running NVT at the experimental density and measuring the pressure? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- Thanks, Jennifer N. -- 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] density off
On 2011-04-20 20.10, Juliette N. wrote: Hi David, I used to apply NPT to fix the density, how can I get the denisty using NVT? You turn off P coupling and fix the right density by scaling using editconf. On 20 April 2011 13:46, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2011-04-20 19.40, Juliette N. wrote: Hello, I am trying to obtain the density for my system that is exactly identical to experimental value but whatever pressure I apply density is still off by 3%. Is this issue common? -- Thanks, Jennifer N. Yes, force fields are not perfect. How about running NVT at the experimental density and measuring the pressure? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Thanks, Jennifer N. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] L-BFGS energy minimization not leading to wrapping of dna around cnt
Dear All, I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure it works) using l-bfgs integrator. When I run in the .trr output file, ends of dna only move slightly towards cnt, but it doesn't wrap around it. Could anyone please guide me what can be the possible issues here, and how can I improve it? Moreover, what is the right value of nstlist for amber99sb-ildn forcefield for md simulations. Thank You, Majid-- 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] L-BFGS energy minimization not leading to wrapping of dna around cnt
majid hasan wrote: Dear All, I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure it works) using l-bfgs integrator. When I run in the .trr output file, ends of dna only move slightly towards cnt, but it doesn't wrap around it. Could anyone please guide me what can be the possible issues here, and how can I improve it? Energy minimization and dynamics are independent processes. You should not expect large structural changes during EM with any of the methods. Moreover, what is the right value of nstlist for amber99sb-ildn forcefield for md simulations. Always start with the primary literature: dx.doi.org/10.1002/prot.22711 -Justin Thank You, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
It is a SunOS operating system, 64 bit with Eight 6-core AMD opteron CPUs. On Wed, Apr 20, 2011 at 11:34 AM, Matthew Zwier mczw...@gmail.com wrote: I've never seen the -D_POSIX_PTHREAD_SEMANTICS before. What caused you to need to define that flag? Also...what hardware (cpu) and operating system (linux? what distro? what version?) are you using? Matt Z. -- 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 -- Ragothaman M Yennamalli, Ph.D. Postdoctoral Research Associate 1012 Crop Genome Informatics Laboratory Department of Genetics, Development and Cell Biology Iowa State University Ames, Iowa 50011-3260 USA +1 515-294-8971 (Office) +1 515-294-8280 (Fax) +1 515-851-1016 (Mobile) When you can do the common things of life in an uncommon way, you will command the attention of the world. -George Washington Carver http://www.gromacs.org/Support/Mailing_Lists http://www.public.iastate.edu/~raghu/ http://www.artistrkrishnarao.com/ *** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
Thanks. I'm no Sun expert, so I'd have to echo Justin's request for the precise sequence of commands you used to install GROMACS and all dependencies. On Wed, Apr 20, 2011 at 2:51 PM, Ragothaman Yennamalli ragotha...@gmail.com wrote: It is a SunOS operating system, 64 bit with Eight 6-core AMD opteron CPUs. On Wed, Apr 20, 2011 at 11:34 AM, Matthew Zwier mczw...@gmail.com wrote: I've never seen the -D_POSIX_PTHREAD_SEMANTICS before. What caused you to need to define that flag? Also...what hardware (cpu) and operating system (linux? what distro? what version?) are you using? Matt Z. -- 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 -- Ragothaman M Yennamalli, Ph.D. Postdoctoral Research Associate 1012 Crop Genome Informatics Laboratory Department of Genetics, Development and Cell Biology Iowa State University Ames, Iowa 50011-3260 USA +1 515-294-8971 (Office) +1 515-294-8280 (Fax) +1 515-851-1016 (Mobile) When you can do the common things of life in an uncommon way, you will command the attention of the world. -George Washington Carver http://www.public.iastate.edu/~raghu/ http://www.artistrkrishnarao.com/ *** -- 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] L-BFGS energy minimization not leading to wrapping of dna around cnt
Okay, thanks. But then does it make any big difference on mdrun if we don't minimize energy first? And one more thing, any idea how long it may take to run md for 367 atoms on a laptop with 2GB ram, and dual core 1.4GHz processor. I am just wondering if it is possible to get any results from mdrun on laptop? Thanks again, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, April 20, 2011 11:47:09 AM Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt majid hasan wrote: Dear All, I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure it works) using l-bfgs integrator. When I run in the .trr output file, ends of dna only move slightly towards cnt, but it doesn't wrap around it. Could anyone please guide me what can be the possible issues here, and how can I improve it? Energy minimization and dynamics are independent processes. You should not expect large structural changes during EM with any of the methods. Moreover, what is the right value of nstlist for amber99sb-ildn forcefield for md simulations. Always start with the primary literature: dx.doi.org/10.1002/prot.22711 -Justin Thank You, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt
majid hasan wrote: Okay, thanks. But then does it make any big difference on mdrun if we don't minimize energy first? You should always run energy minimization. What I'm saying is that you should not expect to see any major changes or important phenomena evolve when simply running EM. And one more thing, any idea how long it may take to run md for 367 atoms on a laptop with 2GB ram, and dual core 1.4GHz processor. I am just wondering if it is possible to get any results from mdrun on laptop? You can get results, but that depends entirely upon how much of the processor is being used to do other things at the same time. For a small system, running locally may be an option, but for anything larger than a few hundred atoms you're better off running on a real cluster to avoid performance loss. It will certainly work, but probably not as fast as you might need for very long simulations. -Justin Thanks again, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wed, April 20, 2011 11:47:09 AM *Subject:* Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt majid hasan wrote: Dear All, I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure it works) using l-bfgs integrator. When I run in the .trr output file, ends of dna only move slightly towards cnt, but it doesn't wrap around it. Could anyone please guide me what can be the possible issues here, and how can I improve it? Energy minimization and dynamics are independent processes. You should not expect large structural changes during EM with any of the methods. Moreover, what is the right value of nstlist for amber99sb-ildn forcefield for md simulations. Always start with the primary literature: dx.doi.org/10.1002/prot.22711 -Justin Thank You, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx segmentation fault
Matthew Zwier wrote: Thanks. I'm no Sun expert, so I'd have to echo Justin's request for the precise sequence of commands you used to install GROMACS and all dependencies. In addition, you can add -g to your CFLAGS to get debugging symbols, then execute pdb2gmx via a debugger like gdb. This should show where the problem is coming from. I have also never used Sun, so I won't be able to comment directly on that, either. -Justin On Wed, Apr 20, 2011 at 2:51 PM, Ragothaman Yennamalli ragotha...@gmail.com wrote: It is a SunOS operating system, 64 bit with Eight 6-core AMD opteron CPUs. On Wed, Apr 20, 2011 at 11:34 AM, Matthew Zwier mczw...@gmail.com wrote: I've never seen the -D_POSIX_PTHREAD_SEMANTICS before. What caused you to need to define that flag? Also...what hardware (cpu) and operating system (linux? what distro? what version?) are you using? Matt Z. -- 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 -- Ragothaman M Yennamalli, Ph.D. Postdoctoral Research Associate 1012 Crop Genome Informatics Laboratory Department of Genetics, Development and Cell Biology Iowa State University Ames, Iowa 50011-3260 USA +1 515-294-8971 (Office) +1 515-294-8280 (Fax) +1 515-851-1016 (Mobile) When you can do the common things of life in an uncommon way, you will command the attention of the world. -George Washington Carver http://www.public.iastate.edu/~raghu/ http://www.artistrkrishnarao.com/ *** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] time of dynamic
Hello gmx-users I have 2 dynamic, one is the continuation of the other. The problem is that both start at time 0.Is there any way to change the dynamic time in order to concatenate both? Thanks in advance. Víctor E. Bahamonde Padilla Laboratorio de Fisicoquímica Molecular Departamento de Química Facultad de Ciencias Universidad de Chile Phone: 562-978-7443 vedua...@ug.uchile.cl -- 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] L-BFGS energy minimization not leading to wrapping of dna around cnt
Okay, thanks a lot. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Wed, April 20, 2011 12:01:33 PM Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt majid hasan wrote: Okay, thanks. But then does it make any big difference on mdrun if we don't minimize energy first? You should always run energy minimization. What I'm saying is that you should not expect to see any major changes or important phenomena evolve when simply running EM. And one more thing, any idea how long it may take to run md for 367 atoms on a laptop with 2GB ram, and dual core 1.4GHz processor. I am just wondering if it is possible to get any results from mdrun on laptop? You can get results, but that depends entirely upon how much of the processor is being used to do other things at the same time. For a small system, running locally may be an option, but for anything larger than a few hundred atoms you're better off running on a real cluster to avoid performance loss. It will certainly work, but probably not as fast as you might need for very long simulations. -Justin Thanks again, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wed, April 20, 2011 11:47:09 AM *Subject:* Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt majid hasan wrote: Dear All, I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure it works) using l-bfgs integrator. When I run in the .trr output file, ends of dna only move slightly towards cnt, but it doesn't wrap around it. Could anyone please guide me what can be the possible issues here, and how can I improve it? Energy minimization and dynamics are independent processes. You should not expect large structural changes during EM with any of the methods. Moreover, what is the right value of nstlist for amber99sb-ildn forcefield for md simulations. Always start with the primary literature: dx.doi.org/10.1002/prot.22711 -Justin Thank You, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] time of dynamic
Víctor Bahamonde wrote: Hello gmx-users I have 2 dynamic, one is the continuation of the other. The problem is that both start at time 0. Is there any way to change the dynamic time in order to concatenate both? trjcat -settime. -Justin Thanks in advance. /Víctor E. Bahamonde Padilla Laboratorio de Fisicoquímica Molecular Departamento de Química Facultad de Ciencias Universidad de Chile Phone: 562-978-7443 vedua...@ug.uchile.cl/ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] restarting from cpt and binary identical
I have a fairly stupid question about restart from a checkpoint and binary identical messages, probably because I can't understand the doco. When I restart (or extend) a double-precision run from a checkpoint involving either dlb or even a different decomposition count (say I changed the number of parallel threads), I get a message that says it restarted but the trajectory is not binary identical. My question is: I assume this trajectory will continue from the last set of double-precision coordinates and velocities in the cpt file? What is the loss in precision/error propagation of the resulting trajectory as compared to if I started the entire run from the begining? (say I am extending my trajectory from 1ns to 10ns). I guess I understand that both trajectories would be equally valid but not binary identical, but what does this mean in terms of things like ultimate RMSD measurements and so forth? I don't necessarily care that the two concatenated trajectory files will not cmp to zero. -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -- 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] restarting from cpt and binary identical
On 4/21/2011 8:00 AM, Peter C. Lai wrote: I have a fairly stupid question about restart from a checkpoint and binary identical messages, probably because I can't understand the doco. When I restart (or extend) a double-precision run from a checkpoint involving either dlb or even a different decomposition count (say I changed the number of parallel threads), I get a message that says it restarted but the trajectory is not binary identical. My question is: I assume this trajectory will continue from the last set of double-precision coordinates and velocities in the cpt file? What is the loss in precision/error propagation of the resulting trajectory as compared to if I started the entire run from the begining? (say I am extending my trajectory from 1ns to 10ns). I guess I understand that both trajectories would be equally valid but not binary identical, but what does this mean in terms of things like ultimate RMSD measurements and so forth? I don't necessarily care that the two concatenated trajectory files will not cmp to zero. These issues are discussed here http://www.gromacs.org/Documentation/Terminology/Reproducibility There's no *loss* upon continuation with a new DD, it's just that it is almost guaranteed to be different from what would have resulted from continuing with the old DD. In the limit of an infinite situation, both would converge to the same ensembles. Makr -- 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] pdb2gmx segmentation fault
Also why the make -j 48, when you only have 8 cores? I'm not even sure if the linker is ok with make -jN for building gromacs, it is not listed as compatible for *BSD ports. Also, does your make (I imagine this is Solaris make) have all the same semantics as gnu-make (gmake)? And why did you switch your CC between fftw and gromacs configures? Solaris 'cc' may or may not be gcc43. Also, do we know if gcc43 is stable especially with -O3...Try removing -O3 or move it to -O2 at most... To rule out a bad fftw library, you can set --with-fft to use the builtin (slower) libfft instead of fftw (but fftw should not be affecting pdb2gmx I don't think...). I too have the questions of your CFLAGS, do you not require -m64 either? On 2011-04-20 10:23:25AM -0500, Ragothaman Yennamalli wrote: On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: Dear Justin, Thanks for the mail. Yes, without these CFLAGS the make was not successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring gromacs. Since without it it would have stopped compiling. I want to agree with you that it is some issue with shared libraries, but i dont think it is the issue since I have used the flag --enable-shared. Also, You did --enable-shared for FFTW, but not Gromacs. Perhaps there is some mismatch there. Since configure did not have any such option, i did not use it. However, I tried compiling with --enable-shared to reinstall gromacs. It installed without any issues. But, the same segmentation fault. if this was the case then editconf would not have worked as well. I wouldn't rule it out just yet. If the installation was successful, everything would work. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 8:33 AM, Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu mailto:jalem...@vt.edumailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: These were the exact commands used to install fftw 3.2.2 ./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared CC=cc F77=f77 make -j 48 make install These were the exact commands used to install gromacs4.5.4 ./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS' I'm no compiler expert, but is it necessary to set all these CFLAGS here? Does the installation fail for some reason if they're not set? Also, how is Gromacs finding FFTW? You haven't set the CPPFLAGS or LDFLAGS. make -j 48 make install I had installed the gromacs version 4.5.3 earlier and encountered the same problem with pdb2gmx. Hence installed the latest version. This would indicate to me that the problem is not necessarily in Gromacs, but the way you're installing it, and as Mark suggested, is probably related to some static/shared library issue. -Justin Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu mailto:jalem...@vt.edumailto:jalem...@vt.edu mailto:jalem...@vt.edumailto:jalem...@vt.edu mailto:jalem...@vt.edumailto:jalem...@vt.edu wrote: Ragothaman Yennamalli wrote: I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect. Any hints will be appreciated. Please provide the exact commands that you used to install Gromacs. What exactly were the issues that you had to circumvent? Have you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4? -Justin Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.orgmailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.orgmailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.orgmailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.orgmailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.orgmailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.orgmailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.orgmailto:gmx-users@gromacs.org
Re: [gmx-users] dhfr-impl-1nm.bench run keeps failing
On 4/20/2011 11:17 PM, Miah Wadud Dr (ITCS) wrote: The MPI library is able to run other MPI jobs as well as other parallel Gromacs runs, and it just seems like this run causes this difficulty. I am using Platform MPI 8.1. OK. That covers just one of the points I raised... Mark -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Wednesday, April 20, 2011 12:46 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dhfr-impl-1nm.bench run keeps failing On 4/20/2011 6:57 PM, Miah Wadud Dr (ITCS) wrote: Hello, I am trying to run the dhfr-impl-1nm.bench benchmark but this keeps failing. I am using Gromacs 4.5.3 built using both Intel and PGI compilers, but both builds fail with the error message: MPI Application rank 1 exited before MPI_Finalize() with status 0 The rank and the status value vary. Any idea what could be wrong? No idea. That's just a generic advisory from the MPI library. Only the mdrun stdout or .log file could have a GROMACS-specific diagnostic message. You need to be sure that you can run other MPI programs, too. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipoles and index file
Hi, I was trying to calculate the dipole moment of part of my peptide. In other words, if I have a 10-residue peptide, I was interested in calculating the dipole-moment contribution of the backbone. So, I made an index file which have a group containing backbone atoms. But, if I try to use g_dipoles to get the dipole moment contribution from the backbone atoms, using following command: g_dipoles -s -f traj -n index.ndx I get an error : --- Program g_dipoles_mod_4mpi, VERSION 4.0.5 Source code file: gmx_dipoles.c, line: 1173 Fatal error: index[1]=197 does not correspond to the first atom of a molecule --- Any help how to get around this will be appreciated. Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] PYP chromophore force field
Hi gromacs users, I am working on Photo active yellow protein. Although i successfully build the force field and patched the chromophore to the protein. After energy minimizing the protein, the chromophore flies away separately. I don't know whether i am missing anything? Please help. Rama -- 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] PYP chromophore force field
Isn't the chromophore supposed to be covalently bonded to the protein? My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al 1994 and van Beeumen et al 1993: This small 125-residue protein contains a p-coumaric acid chromophore that is covalently bound to the protein backbone via a thiol-ester cysteine linkage Cys-69... Maybe you forgot to specify a covalent bond in your topology... On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote: Hi gromacs users, I am working on Photo active yellow protein. Although i successfully build the force field and patched the chromophore to the protein. After energy minimizing the protein, the chromophore flies away separately. I don't know whether i am missing anything? Please help. Rama -- 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 -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -- 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] PYP chromophore force field
Yes, you are right, the chromophore(p-coumaric acid) is covalently bonded to the Sulphur(S) atom of the Cys-69 residue. But I specified the covalent bond in my topology. [ bonds] C +SG [ angles ] OC +SG CA1 C +SG C +SG +CB [ dihedrals ] O C +SG+CB CA1C +SG+CB HA2 CA1 C +SG CA2 CA1 C +SG C +SG +CB +CA C +SG +CB +HB1 C +SG +CB +HB2 After doing pdb2gmx, i got the right structure. But the chromophore flies away after minimising. Thanks Rama On Wed, Apr 20, 2011 at 4:57 PM, Peter C. Lai p...@uab.edu wrote: Isn't the chromophore supposed to be covalently bonded to the protein? My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al 1994 and van Beeumen et al 1993: This small 125-residue protein contains a p-coumaric acid chromophore that is covalently bound to the protein backbone via a thiol-ester cysteine linkage Cys-69... Maybe you forgot to specify a covalent bond in your topology... On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote: Hi gromacs users, I am working on Photo active yellow protein. Although i successfully build the force field and patched the chromophore to the protein. After energy minimizing the protein, the chromophore flies away separately. I don't know whether i am missing anything? Please help. Rama -- 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 -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -- 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] problem with g_dipoles and index file
Hi, I was trying to calculate the dipole moment of part of my peptide. In other words, if I have a 10-residue peptide, I was interested in calculating the dipole-moment contribution of the backbone. So, I made an index file which have a group containing backbone atoms. But, if I try to use g_dipoles to get the dipole moment contribution from the backbone atoms, using following command: g_dipoles -s -f traj -n index.ndx I get an error : --- Program g_dipoles_mod_4mpi, VERSION 4.0.5 Source code file: gmx_dipoles.c, line: 1173 Fatal error: index[1]=197 does not correspond to the first atom of a molecule --- Any help how to get around this will be appreciated. Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] PYP chromophore force field
On 4/21/2011 10:12 AM, Ramachandran G wrote: Yes, you are right, the chromophore(p-coumaric acid) is covalently bonded to the Sulphur(S) atom of the Cys-69 residue. But I specified the covalent bond in my topology. [ bonds] C +SG That's your .rtp entry. What's in your [molecules] section of your topology? Mark [ angles ] OC +SG CA1 C +SG C +SG +CB [ dihedrals ] O C +SG+CB CA1C +SG+CB HA2 CA1 C +SG CA2 CA1 C +SG C +SG +CB +CA C +SG +CB +HB1 C +SG +CB +HB2 After doing pdb2gmx, i got the right structure. But the chromophore flies away after minimising. Thanks Rama On Wed, Apr 20, 2011 at 4:57 PM, Peter C. Lai p...@uab.edu mailto:p...@uab.edu wrote: Isn't the chromophore supposed to be covalently bonded to the protein? My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al 1994 and van Beeumen et al 1993: This small 125-residue protein contains a p-coumaric acid chromophore that is covalently bound to the protein backbone via a thiol-ester cysteine linkage Cys-69... Maybe you forgot to specify a covalent bond in your topology... On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote: Hi gromacs users, I am working on Photo active yellow protein. Although i successfully build the force field and patched the chromophore to the protein. After energy minimizing the protein, the chromophore flies away separately. I don't know whether i am missing anything? Please help. Rama -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- === Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu mailto:p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 tel:%28205%29%20690-0808 | === -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with g_dipoles and index file
On 4/21/2011 10:17 AM, Sanku M wrote: Hi, I was trying to calculate the dipole moment of part of my peptide. In other words, if I have a 10-residue peptide, I was interested in calculating the dipole-moment contribution of the backbone. So, I made an index file which have a group containing backbone atoms. But, if I try to use g_dipoles to get the dipole moment contribution from the backbone atoms, using following command: g_dipoles -s -f traj -n index.ndx I get an error : --- Program g_dipoles_mod_4mpi, VERSION 4.0.5 Source code file: gmx_dipoles.c, line: 1173 Fatal error: index[1]=197 does not correspond to the first atom of a molecule --- Calculating a dipole moment of a possibly-charged species requires that there be a reference point, which is conventionally the center of mass of the molecule. This means all the atoms of the molecule have to be known, and g_dipoles assumes the index group consists of whole molecules. So to do the partition you want, you will need to provide the same molecules, but with zero charges on the non-backbone atoms. That will mean making a copy of your .top and hacking those charges to zero to generate a new such .tpr. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with g_dipoles and index file
On 4/21/2011 10:33 AM, Mark Abraham wrote: On 4/21/2011 10:17 AM, Sanku M wrote: Hi, I was trying to calculate the dipole moment of part of my peptide. In other words, if I have a 10-residue peptide, I was interested in calculating the dipole-moment contribution of the backbone. So, I made an index file which have a group containing backbone atoms. But, if I try to use g_dipoles to get the dipole moment contribution from the backbone atoms, using following command: g_dipoles -s -f traj -n index.ndx I get an error : --- Program g_dipoles_mod_4mpi, VERSION 4.0.5 Source code file: gmx_dipoles.c, line: 1173 Fatal error: index[1]=197 does not correspond to the first atom of a molecule --- Calculating a dipole moment of a possibly-charged species requires that there be a reference point, which is conventionally the center of mass of the molecule. This means all the atoms of the molecule have to be known, and g_dipoles assumes the index group consists of whole molecules. So to do the partition you want, you will need to provide the same molecules, but with zero charges on the non-backbone atoms. That will mean making a copy of your .top and hacking those charges to zero to generate a new such .tpr. Actually, tpbconv has the ability to set the charges of a group in a .tpr to zero. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] dna and cnt get distorted in md simulation
Dear All, I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. My commands are: For energy minimization, grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd and then I ran molecular dyamics, grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd For individual DNA, and CNT alone, both produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, both energy minimization and mdrun lead to distorted structures: bond lengths don't remain fixed neither for CNT nor for DNA, and atoms of both molecules get intertwined and produce a mess. I tried two .mdp files. I got the first .mdp from a colleague who used it for a simple simulation of CNT only (without solvent, and any other molecule) . I made few changes in this file after going through manual e.g enabled free energy calculations, added nsttcouple = -1 value, changed valued of comm_mode from Angular to Linear, changed ns_type value from grid to simple, changed rcoulomb and rvdw values from 0.9 to 1, Both .mdp files are placed at following addresses: http://phas.ubc.ca/~majid/md.mdp (first .mdp file) http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file) It seems to me that problem might be related to non-bonded interaction because this is the significant difference between one and two molecule system. Any help would be much appreciated. Thanks, Majid-- 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
