[gmx-users] regarding charge group
The sum of the two largest charge group radii (13.336) is larger than rlist(1.2) - rvdw/rcoulomb i am getting this error while running membrane simulations. please any one suggest how to rectify this error. -- regards M.SathishKumar -- 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] regarding charge group
Probably, make your broken molecules whole before passing them to grompp. Mark On Tue, Oct 22, 2013 at 8:26 AM, Sathish Kumar sathishk...@gmail.comwrote: The sum of the two largest charge group radii (13.336) is larger than rlist(1.2) - rvdw/rcoulomb i am getting this error while running membrane simulations. please any one suggest how to rectify this error. -- regards M.SathishKumar -- 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] Minimum distance between periodic images
Dear all users I have simulated a protein with two chains (153 residues each) for 50ns(restarting crashed run 3 times) using a cubic box with each side as 11nm. After finding the closest distance between the periodic images, I found that the closest distance becomes lesser than 1 after 23ns for few ns and then again shoots up (and fluctuates around the previous value) and then again becomes lesser than 1 around 49ns.The command which I used: g_mindist -f md-run-1-noPBC.xtc -s md-run-1.tpr -n index.ndx -od mindist.xvg -pi Similar trend is seen when I plotted rmsd curve and distance between the two chains or any other analysis curve (ie at those specific time intervals in between, the value shoots up) My question is : Will it be reasonable enough to carry out my analysis for first 22ns and discard the rest? Is this the problem due to smaller box size or some other parameter as the previous studies (through literature survey) have used even much lesser box length (although their simulations were also of short duration than 50ns). I have posted the output of minimum distance between periodic images at : https://plus.google.com/photos/109332801667278171972/albums/5937501788329595121?authkey=CJHD-9XO7dH4jgE and rmsd wrt c alpha at : https://plus.google.com/photos/109332801667278171972/albums/5937501062407227393?authkey=CKOE9sP5pMO2NA Please help me figure out the problem. Thanks in advance. -- 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] Minimum distance between periodic images
Hi Nidhi, These are periodicity artifacts. Make sure that you remove jumps over PBC from your trajectory by using trjconv -pbc nojump. Cheers, Tsjerk On Tue, Oct 22, 2013 at 11:14 AM, Nidhi Katyal nidhikatyal1...@gmail.comwrote: Dear all users I have simulated a protein with two chains (153 residues each) for 50ns(restarting crashed run 3 times) using a cubic box with each side as 11nm. After finding the closest distance between the periodic images, I found that the closest distance becomes lesser than 1 after 23ns for few ns and then again shoots up (and fluctuates around the previous value) and then again becomes lesser than 1 around 49ns.The command which I used: g_mindist -f md-run-1-noPBC.xtc -s md-run-1.tpr -n index.ndx -od mindist.xvg -pi Similar trend is seen when I plotted rmsd curve and distance between the two chains or any other analysis curve (ie at those specific time intervals in between, the value shoots up) My question is : Will it be reasonable enough to carry out my analysis for first 22ns and discard the rest? Is this the problem due to smaller box size or some other parameter as the previous studies (through literature survey) have used even much lesser box length (although their simulations were also of short duration than 50ns). I have posted the output of minimum distance between periodic images at : https://plus.google.com/photos/109332801667278171972/albums/5937501788329595121?authkey=CJHD-9XO7dH4jgE and rmsd wrt c alpha at : https://plus.google.com/photos/109332801667278171972/albums/5937501062407227393?authkey=CKOE9sP5pMO2NA Please help me figure out the problem. Thanks in advance. -- 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. -- 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] Regarding membrane(DMPC) simulations with fullerene
Dear Sir, I am doing fullerene interaction with DMPC , i downloaded the gro file from the website mentioned in the tutorial. I was keep the fullerene on the top of DMPC. But in the gro file already water is present. If i removed that water molecules and adding new water molecules by using genbox command and afetr the running energy minimization the lipid structure was collapsed. it is not like initial structure and some gaps were found in the middle of membrane. By keeping the water molecules as such from the gro file and i keep the fullerene above the membrane then the presented water molecules were randomly distributed inside the membrane, and structure of water was distrubed. If i added water using genbox to the membrane( with water from gro file), there is a seperation found between two water layers. Energy minimization was not running in all above cases. How can i run this simulation please suggest me Is there any tutorial like this simulation. Thank You. -- regards M.SathishKumar -- 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] Minimum distance between periodic images
Thank you sir. On Tue, Oct 22, 2013 at 2:48 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Nidhi, These are periodicity artifacts. Make sure that you remove jumps over PBC from your trajectory by using trjconv -pbc nojump. Cheers, Tsjerk On Tue, Oct 22, 2013 at 11:14 AM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Dear all users I have simulated a protein with two chains (153 residues each) for 50ns(restarting crashed run 3 times) using a cubic box with each side as 11nm. After finding the closest distance between the periodic images, I found that the closest distance becomes lesser than 1 after 23ns for few ns and then again shoots up (and fluctuates around the previous value) and then again becomes lesser than 1 around 49ns.The command which I used: g_mindist -f md-run-1-noPBC.xtc -s md-run-1.tpr -n index.ndx -od mindist.xvg -pi Similar trend is seen when I plotted rmsd curve and distance between the two chains or any other analysis curve (ie at those specific time intervals in between, the value shoots up) My question is : Will it be reasonable enough to carry out my analysis for first 22ns and discard the rest? Is this the problem due to smaller box size or some other parameter as the previous studies (through literature survey) have used even much lesser box length (although their simulations were also of short duration than 50ns). I have posted the output of minimum distance between periodic images at : https://plus.google.com/photos/109332801667278171972/albums/5937501788329595121?authkey=CJHD-9XO7dH4jgE and rmsd wrt c alpha at : https://plus.google.com/photos/109332801667278171972/albums/5937501062407227393?authkey=CKOE9sP5pMO2NA Please help me figure out the problem. Thanks in advance. -- 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. -- 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] a new GROMACS simulation tool
Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- 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] a new GROMACS simulation tool
Is there a link to the documentation? It's a little difficult to know exactly what this supposed to be doing. Is it a GUI interface to gromacs? In general, it would be great to get these sort of extensions coordinated with the main gromacs development tree, since otherwise they would tend to get out of sync, lowering utility to everyone. On Tue, Oct 22, 2013 at 10:34 AM, Kevin Chen fch6...@gmail.com wrote: Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- 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] Problems about the output force
Dear all, I have some doubt for the output force. What contributions do the output forces in .trr file include? Certainly, the pair forces and bonded interactions are included. However, if the external field (such as electric field) is applied, is the external force included? In addition, if the constraint (such as LINCS or SHAKE constraints) is used, is it also included in the output force? If so, how is the constraint contribution calculated? Best, Qianqian -- 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] a new GROMACS simulation tool
Hi Michael, Sorry, if this is not the right place to post message of such. To answer your question, it is a web-based GUI interface to GROMACS, which is a perfect fit for those who are trying to learn MD or to run large scale protein simulations on HPC. Best Regards, KevinFeng Chen, Ph.D. XSEDE Campus Champion, XSEDE Extended Collaborative Support (ECSS) Consultant and Research Programmer Rosen Center for Advanced Computing Information Technology at Purdue (ITaP) Young Hall,RM 952 155 South Grant Street West Lafayette, IN 47907-2108 off: (765) 496-9614 fax: (765) 496-4295 -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Michael Shirts Sent: Tuesday, October 22, 2013 1:18 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] a new GROMACS simulation tool Is there a link to the documentation? It's a little difficult to know exactly what this supposed to be doing. Is it a GUI interface to gromacs? In general, it would be great to get these sort of extensions coordinated with the main gromacs development tree, since otherwise they would tend to get out of sync, lowering utility to everyone. On Tue, Oct 22, 2013 at 10:34 AM, Kevin Chen fch6...@gmail.com wrote: Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- 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 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] Regarding membrane(DMPC) simulations with fullerene
On 10/22/13 9:15 AM, Sathish Kumar wrote: Dear Sir, I am doing fullerene interaction with DMPC , i downloaded the gro file from the website mentioned in the tutorial. I was keep the fullerene on the top of DMPC. But in the gro file already water is present. If i removed that water molecules and adding new water molecules by using genbox command and afetr the running energy minimization the lipid structure was collapsed. it is not like initial structure and some gaps were found in the middle of membrane. By keeping the water molecules as such from the gro file and i keep the fullerene above the membrane then the presented water molecules were randomly distributed inside the membrane, and structure of water was distrubed. If i added water using genbox to the membrane( with water from gro file), there is a seperation found between two water layers. All of the above outcomes simply suggest that you're not building the system in a sensible manner. Without exact commands and some images of what you're getting, there's nothing that anyone can really do to help. Energy minimization was not running in all above cases. How can i run this simulation please suggest me Is there any tutorial like this simulation. If it's not linked on the Gromacs website and Google can't find it, then no. Tutorials don't exist for every iteration of a task. You want to place a molecule at some location relative to a membrane; that's not significantly different from the simple concepts described here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/03_tricks.html -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Conflicting atom names when using g_density
Hi Everyone, I am having an awkward situation. I want to use g_density to get the density profile of a lipid bilayer. At first glance, it looks like a trivial task. But for my case, it's not because I have conflicting atom names from two different molecules. I am using GROMOS 53a6. In DPPC topology, I have C1 C2 C3 N4...O7... In another lipid topology, say lipid B, I have C1 C2 C3 N4... C7... The C1 in DPPC and C1 in lipid B could have different atomic mass as GROMOS is united atom representation. C1 of DPPC could be a CH2, C2 of lipid B could be a CH3. Then I don't know how to specify the entry in the .dat file: C1 = ? Is it possible to calculate the density profile of the whole bilayer by just invoking g_density once? Or in my awkward situation, I have to calculate the density profile of each molecule type, then add them together? Then I will be concerned with the numerical errors involved. Thanks. Bin -- 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] Conflicting atom names when using g_density
On 10/22/13 9:05 PM, Bin Liu wrote: Hi Everyone, I am having an awkward situation. I want to use g_density to get the density profile of a lipid bilayer. At first glance, it looks like a trivial task. But for my case, it's not because I have conflicting atom names from two different molecules. I am using GROMOS 53a6. In DPPC topology, I have C1 C2 C3 N4...O7... In another lipid topology, say lipid B, I have C1 C2 C3 N4... C7... The C1 in DPPC and C1 in lipid B could have different atomic mass as GROMOS is united atom representation. C1 of DPPC could be a CH2, C2 of lipid B could be a CH3. Then I don't know how to specify the entry in the .dat file: C1 = ? Is it possible to calculate the density profile of the whole bilayer by just invoking g_density once? Or in my awkward situation, I have to calculate the density profile of each molecule type, then add them together? Then I will be concerned with the numerical errors involved. Assign unique names in the .top, create a new .tpr, and the problem is solved. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102
Hi!
It is strange but such combination works:
CC=icc CXX=icpc ~/cmake-2.8.12/bin/cmake ..
-DCMAKE_INSTALL_PREFIX=/ifs/apps/GROMACS-4.6.3 -DGMX_X11=OFF
-DGMX_MPI=ON -DGMX_FFT_LIBRARY=mkl -DGMX_GPU=ON cmake.log
It was a command that our cluster administrator was able to configure
GROMACS with. So the problem has been solved.
16.10.2013 18:17, Mark Abraham пишет:
On Wed, Oct 16, 2013 at 12:27 PM, Nikolay Alemasov suc...@gmail.com wrote:
Thank you, Mark!
It was already tried. I mean a fresh unpacking and further cmake run.
As for your first thought concerning a loss of access to some parts of
gmxlib:
[alemasov@nks-g6 gromacs-4.6.3]$ ls -l ./src/gmxlib/ | grep -e - | cut
-d' ' -f 1 | sort -n | uniq
drwxr-x---
-rw-r-
So there are only two permissions patterns which allow me to
read/write items in the directory. I am little bit confused. Are there any
limitations about OS or cmake versions? The latter is cmake version
2.8.12.
Also relevant are the owners, if you have unpacked as root and built as
normal user, or vice-versa, etc. You should be doing nothing with root
until you need to install, of course, and since you are installing to user
space, you definitely should not be root.
CMake has not yet updated their compatibility matrix for 2.8.12 (
http://www.cmake.org/Wiki/CMake_Version_Compatibility_Matrix/Commands) and
as you can see there, things that used to work occasionally stop working.
If you can try a different version of CMake we can rule out bugs in CMake
2.8.12.
Mark
(Redirected from gmx-developers)
The only way I can reproduce those symptoms is if I delete (or otherwise
make unreadable) various parts of src/gmxlib. You may have deleted some
files or been a different user at some point. I suggest you do a fresh
unpack of the tarball and try again.
Mark
On Wed, Oct 16, 2013 at 7:19 AM, Nikolay Alemasov such3r at gmail.com
http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
wrote:
/ Greetings,
//
// I am trying to compile the source code v.4.6.3 with cmake. The
shell
// script is (ran from the build directory inside gromacs source root
dir):
//
// CC=/ifs/opt/2013/intel/bin/icc
// CXX=/ifs/opt/2013/intel/bin/icpc
// CMAKE_PREFIX_PATH=/ifs/home/bionet/alemasov/libraries/
fftw
//
// cmake .. \
// -DGMX_GPU=OFF \
// -DGMX_CPU_ACCELERATION=SSE2 \
// -DFFTWF_LIBRARY='/ifs/home/bionet/alemasov/libraries/
fftw/lib/libfftw3f.so'
// \
// -DFFTWF_INCLUDE_DIR='/ifs/home/bionet/alemasov/
libraries/fftw/include'
// \
// -DCMAKE_INSTALL_PREFIX='/ifs/home/bionet/alemasov/
libraries/gromacs'
//
//
// And get a message (successful part was cut):
// ...
//
// -- Performing Test HAVE_DLOPEN
// -- Performing Test HAVE_DLOPEN - Success
// -- Checking for dlopen - found
// -- Found the ability to use plug-ins when building shared libaries,
so
// will compile to use plug-ins (e.g. to read VMD-supported file
formats).
// -- Checking for suitable VMD version
// -- VMD plugins not found. Path to VMD can be set with VMDDIR.
// CMake Error at src/gmxlib/CMakeLists.txt:102 (list):
//list sub-command REMOVE_ITEM requires two or more arguments.
//
//
// CMake Error at src/gmxlib/CMakeLists.txt:105 (list):
//list sub-command REMOVE_ITEM requires two or more arguments.
//
//
// You have called ADD_LIBRARY for library md without any source
files. This
// typically indicates a problem with your CMakeLists.txt file
// -- Configuring incomplete, errors occurred!
// See also /ifs/home/bionet/alemasov/
libraries/gromacs-4.6.3/build/
// CMakeFiles/CMakeOutput.log.
// See also /ifs/home/bionet/alemasov/
libraries/gromacs-4.6.3/build/
// CMakeFiles/CMakeError.log.
//
//
// Below is a content of the src/gmxlib/CMakeLists.txt:99-105:
//
// 99 : # Files called xxx_test.c are test drivers with a main()
function
// for module xxx.c,
// 100: # so they should not be included in the library
// 101: file(GLOB_RECURSE NOT_GMXLIB_SOURCES *_test.c *\#*)
// 102: list(REMOVE_ITEM GMXLIB_SOURCES ${NOT_GMXLIB_SOURCES})
// 103: # Selection has test_ instead of _test.
// 104: file(GLOB SELECTION_TEST selection/test*)
// 105: list(REMOVE_ITEM GMXLIB_SOURCES ${SELECTION_TEST})
//
//
// The target system:
//
// Linux nks-g6.sscc.ru 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT
2009
// x86_64 x86_64 x86_64 GNU/Linux
// Red Hat Enterprise Linux Server release 5.4 (Tikanga)
// model name: Intel(R) Xeon(R) CPU X5560 @ 2.80GHz
//
//
// Please help me to sort out the issue. In fact my primary aim was to
build
// GPU-version of the GROMACS, but I can not do it even for the simplest
// variant.
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[gmx-users] Energy minimizations taking really, really long?
I have some simulations of inserting a probe molecule into a bilayer. Some molecules work fine. However, a certain class of molecules is taking an absurdly long time to run the exact same simulation, even though I energy minimized the molecules individually beforehand and there are no overlaps. What might be going wrong? Thanks. -- 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] Box size increases in NPT
Hello, I am running a NPT simulation for cyclopropylchloride(1) in 50%water(100)+50%ethanol(100) using opls force field parameter . After equilibration box size increases from 20 A to 70 A. I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 5 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 290;350 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Free energy control stuff free_energy = no Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Energy minimizations taking really, really long?
It depending the time steps that u used or the molecule that u had is big..Thats why ur EM take a long time..Is better take a long time rather than quick but had a lot of errors.. On Wed, Oct 23, 2013 at 9:59 AM, Nimmy McNimmerson [via GROMACS] ml-node+s5086n5011918...@n6.nabble.com wrote: I have some simulations of inserting a probe molecule into a bilayer. Some molecules work fine. However, a certain class of molecules is taking an absurdly long time to run the exact same simulation, even though I energy minimized the molecules individually beforehand and there are no overlaps. What might be going wrong? Thanks. -- gmx-users mailing list[hidden email] 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 [hidden email]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/Energy-minimizations-taking-really-really-long-tp5011918.html To start a new topic under GROMACS Users Forum, email ml-node+s5086n4370410...@n6.nabble.com To unsubscribe from GROMACS, click here. NAML -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my -- View this message in context: http://gromacs.5086.x6.nabble.com/Energy-minimizations-taking-really-really-long-tp5011918p5011919.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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] Continuing runs from 4.5.4 in 4.6.3
Hi, We recently had a software upgrade in our cluster from gromacs 4.5.4. to gromacs 4.6.3.. I need to continue an earlier simulation that had been run in 4.5.4. using the .cpt, .tpr and .mdp. Are there any issues with continuing these runs in 4.6.3.? Can I concatenate these trajectories for later analysis? I notice that I cannot use a 4.6.3 .cpt and .tpr in 4.5.4. Any input will be appreciated. Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
