[gmx-users] On the choosing of GPU for MD runs
Dear Gromacs Users! I wounder to know some detailes about choosing of the gpu for md with gromacs. In particular on what properties of the videoadapter should I pay most attention ? What modern gpu nvidia-series might give best performance (gtx 6xx, tesla or quadro series) ? Could you provide me with some bechmarks besides the information present on the Gromacs web ? For instance with the gpu Geforce GTX 670 + core i5 (4 cores) I have performance 10ns\day for explicit system with 67000 atoms ( protein in tip3p water). Have someone better results with common home-like desktop? :) James -- 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] activation energy
Dear users, Is it possible to calculate the activation energy of a structure using Gromacs? if OK, how? Thanks in advance -- Ahmet Yıldırım -- 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] activation energy
I would first explain what do you mean with activation energy. What definition do you use? On 01/14/2013 01:15 PM, Ahmet yıldırım wrote: Dear users, Is it possible to calculate the activation energy of a structure using Gromacs? if OK, how? 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] activation energy
It is the minimum energy required to start a chemical reaction. I have a structure complexed A and B ligands. I want to calculate how these ligands changed the activation energy. 2013/1/14 Felipe Pineda, PhD luis.pinedadecas...@lnu.se I would first explain what do you mean with activation energy. What definition do you use? On 01/14/2013 01:15 PM, Ahmet yıldırım wrote: Dear users, Is it possible to calculate the activation energy of a structure using Gromacs? if OK, how? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- 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] activation energy
On 01/14/2013 01:29 PM, Ahmet yıldırım wrote: It is the minimum energy required to start a chemical reaction. OK. In a chemical reaction bonds are built or broken. None of this happens during a MD simulation. I have a structure complexed A and B ligands. I want to calculate how these ligands changed the activation energy. You would probably need some kind of (ab-initio) QM calculation to study this. It would be a better idea to ask, e.g., the Gaussian community (in CCL) for advice. 2013/1/14 Felipe Pineda, PhD luis.pinedadecas...@lnu.se I would first explain what do you mean with activation energy. What definition do you use? On 01/14/2013 01:15 PM, Ahmet yıldırım wrote: Dear users, Is it possible to calculate the activation energy of a structure using Gromacs? if OK, how? 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] DD cells - regd
On Sat, Jan 12, 2013 at 10:04 AM, ramesh cheerla rameshgrom...@gmail.com wrote: This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells This gives another possible solution. You decrease the number of DD grid cells by reducing the numbers of cores on which mdrun runs. Or, for the same number of cores, you can control better the decomposition using the '-dd' option in case the constraints are aligned to one of the 3 main directions. Cheers, Bogdan -- 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] PBC for evaporation of droplets?
Dear all, I would like to ask you that using PBC for evaporation of droplets is necessary? Please note that the MD simulations are to be performed in vacuum. I checked the relevant references but in some of them PBC has been taken into account but in others not [for instance please see J.chem. phys. 125, 154508 (2006) and J. chem. phys. 134, 164309 (2011)]. I would be grateful if you can tell me advantages and disadvantages of PBC in evaporation of droplets in the vacuum. Best regards Rasoul -- 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] Covariance analysis of X-ray ensemble
Hello. Check your topology file. You should have had a mistake in matching the atoms. Best regards. Lucio. El vie, 11-01-2013 a las 21:46 +0300, James Starlight escribió: Tsjerk, thanks for suggestion! By the way I've found in the pca.log ( that time pca was done on trajectory as well as TRP ( not pdb) files as the inputs ): Read 30 frames from cam_xray_coors_bb.pdb (time 1 to 30 ps) Read reference structure for fit from x_ray.tpr Analysis group is 'System' (575 atoms) Fit group is 'System' (575 atoms) Analysis is non-mass weighted Fit is non-mass weighted Diagonalized the 1725x1725 covariance matrix Trace of the covariance matrix before diagonalizing: 350.847 Trace of the covariance matrix after diagonalizing: 350.847 Wrote 1725 eigenvalues to PCA_eigenval.xvg Wrote reference structure to PCA_eigenvec.trr Wrote average structure to PCA_average.pdb and PCA_eigenvec.trr Wrote eigenvectors 1 to 29 to PCA_eigenvec.trr It seems that cov.analysis was done also as non-mass weighted. Actualy I extract eigenvectors for further essential dynamics sampling runs. In the literature I've found that for EDA eigenvectors from only non-mass weighted PCA are suitable. So if its true in what cases mass weighted eigenvectors might be used? James 2013/1/11 Tsjerk Wassenaar tsje...@gmail.com: Hi James, You don't need a .tpr file. A .gro or .pdb file will do as well. Unless you insist on doing mass-weighted PCA. Cheers, Tsjerk On Fri, Jan 11, 2013 at 4:04 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs users! I want to perform Covariance analysis of my x-ray data sets via g_covar -f trr.pdb -s x_ray.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr where trr.pdb is the trajectory made from the 30 x-ray structures (only c-alpha atoms were selected. How I could obtain x_ray.tpr file for such analysis? I've tried to use tpr from full atomic model of the same protein which I';ve simulated recently. For that p[rotein tpr file have been already created. From that model via make_ndx I've defined only backbone atoms corresponded to the atoms in my pdb ensemble. On the next step I've used tpbconv on protein.tpr with index file to make reduced tpr file with atoms corresponded to the backbone of the pdb-ensemble. Now when I run g_covar with my ensemble and reduced tpr file I obtain error *** glibc detected *** g_covar: malloc(): memory corruption: 0x7f27df53e018 *** On other hand if I specify for g_covar full-atomic tpr file with the index ( where atoms corresponded to the trr.pdb are mentioned) g_covar -f trr.pdb -s protein.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr I obtain another error Calculating the average structure ... Reading frame 0 time1.000 WARNING: number of atoms in tpx (575) and trajectory (575) do not match --- Program g_covar, VERSION 4.5.5 Source code file: /tmp/build/gromacs-4.5.5/src/gmxlib/mshift.c, line: 102 Fatal error: Molecule in topology has atom numbers below and above natoms (575). You are probably trying to use a trajectory which does not match the first 575 atoms of the run input file. What I've done wrong and how I can define tpr file for trajectory made from several pdb files ? Thanks for help James -- 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 Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: On the choosing of GPU for MD runs
1)As I understood from nvidia site at present time GPU's from the tesla serie are the best for the calculations like md. For instasnce NVIDIA Tesla C2075 have performance ~ 1 TFLOPS in the single-precission calculations. I wounder to know how many 8-core CPU must have typical cluster to obtain such performance ? Have someone tried to use tesla GPU with gromacs ? What real performance in ns\day have been obtained with the explicit solvent systems? 2) Today I performed test gpu-based calculation with 2 different gpu's ( GTX 670 vs GT 640). Both of that gpu's have the same GPU frequency but GTX 670 has 256 bit memory interface width with ddr5 ram worked on higher frequency. As the result I've obtained 50% more perfomance with the GTX 670. Does the memory interface width as well as ram frequency affect on total GPU performance in addition to GPU frequency? James 2013/1/14 James Starlight jmsstarli...@gmail.com: Dear Gromacs Users! I wounder to know some detailes about choosing of the gpu for md with gromacs. In particular on what properties of the videoadapter should I pay most attention ? What modern gpu nvidia-series might give best performance (gtx 6xx, tesla or quadro series) ? Could you provide me with some bechmarks besides the information present on the Gromacs web ? For instance with the gpu Geforce GTX 670 + core i5 (4 cores) I have performance 10ns\day for explicit system with 67000 atoms ( protein in tip3p water). Have someone better results with common home-like desktop? :) James -- 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] Turn on pdb output after every step
Hello For some reasons, I want to output pdb file output after every step of the MD run. After searching the forum, I found that Gromacs does that only in some circumstances(like when the system is about to crash or already crashed). http://gromacs.5086.n6.nabble.com/turn-off-pdb-output-td4417229.html#a4417301 Is there a way I could have a control on that by changing a flag and can I write only the protein part ignoring the solvent? Thanks Santhosh -- View this message in context: http://gromacs.5086.n6.nabble.com/Turn-on-pdb-output-after-every-step-tp5004542.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
Re: [gmx-users] Turn on pdb output after every step
On 1/14/13 3:02 PM, santhosh wrote: Hello For some reasons, I want to output pdb file output after every step of the MD run. After searching the forum, I found that Gromacs does that only in some circumstances(like when the system is about to crash or already crashed). http://gromacs.5086.n6.nabble.com/turn-off-pdb-output-td4417229.html#a4417301 Is there a way I could have a control on that by changing a flag and can I write only the protein part ignoring the solvent? Why not just set nstxtcout = 1 with xtc-grps = Protein? trjconv -sep will then write separate coordinate files in whatever format you choose after the run. Anything else would require modification of the code. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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: Turn on pdb output after every step
@Justin : Thanks for your time but I think I was a little unclear. I want to output pdb during the run. Before every integration step, I want to output the current configuration of the system. (This would make the system slow but right now thats not my concern). -- View this message in context: http://gromacs.5086.n6.nabble.com/Turn-on-pdb-output-after-every-step-tp5004542p5004544.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
Re: [gmx-users] Re: Turn on pdb output after every step
On 1/14/13 3:23 PM, santhosh wrote: @Justin : Thanks for your time but I think I was a little unclear. I want to output pdb during the run. Before every integration step, I want to output the current configuration of the system. (This would make the system slow but right now thats not my concern). Then, as I said, you will likely have to modify the code. The emergency dump of .pdb files is probably not going to be useful in any way, and the environment variable that controls its behavior only turns it off, not on. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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: Adding a new water model to gromacs
On 1/14/13 9:04 PM, learnmd wrote: Justin, Thanks for the direction. So, I have now edited spc template to create a new model called spchw. The spchw.itp for amber99 forcefield now looks like this: [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; id at type res nr res name at name cg nr chargemass 1 OW_spch 1 SOL OW 1 -0.870 15.99940 2 HW_spch 1 SOL HW1 1 0.4352.00800 3 HW_spch 1 SOL HW2 1 0.4352.00800 #ifndef FLEXIBLE [ settles ] ; OW funct doh dhh 1 1 0.1 0.16330 [ exclusions ] 1 2 3 2 1 3 3 1 2 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.1 345000 0.1 345000 1 3 1 0.1 345000 0.1 345000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 109.43 383 109.47 383 #endif I have also edited the ffnonbonded.itp file for amber99 to include this model atomtypes ] ; name at.num mass charge ptype sigma epsilon Br 35 79.900. A 0.0e+00 0.0e+00 ; spch water - use only with spch.itp settles OW_spch 8 15.9994 0. A 3.16557e-01 6.50629e-01 HW_spch 1 2.0080 0. A 0.0e+00 0.0e+00 Please advise if this is sufficient. In principle. Try it and see. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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] make a movie from vmd
On 1/14/13 9:22 PM, Nur Syafiqah Abdul Ghani wrote: Hi guys, Can you suggest me how to make a movie from the vmd to the slide presentation? Well, when I opened the trajectories of the protien with xtc file it show the movement.But how i can save it as a movie to present with other peoples? VMD has several tutorials for making movies - apply Google here. There's a VMD mailing list that is more appropriate for these questions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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
