Re: [gmx-users] Re: slow speed
Justin is correct the benchmark is not necessarily what you want to reproduce or use one of the setups used. Then 1 steps in 10 mn that gets you 10 ps/10 mn, so 10*6*24=1,440 ps/day, depending on your system this might actually be fine. You use SD, I am not sure this will result in the same performance as md! Do you have solvent? Note that there are funny things in your md file. eg: nstlist = 50 is certainly something you don't want to keep for production. XAvier. On Apr 16, 2010, at 1:47 AM, Justin A. Lemkul wrote: Shuangxing Dai wrote: I am not running in parallel. Right now I just changed links order from 12 to 4. It is still slow. While I change to shift, not Ewald, it finished 1 steps in 10 mins. In the paper: J Comput Chem. javascript:AL_get(this,%20'jour',%20'J%20Comput%20Chem.'); 2005 Dec;26(16):1701-18. GROMACS: fast, flexible, and free. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.103.418rep=rep1type=pdf Van Der Spoel D http://www.ncbi.nlm.nih.gov/pubmed?term=%22Van%20Der%20Spoel%20D%22%5BAuthor%5D , Lindahl E http://www.ncbi.nlm.nih.gov/pubmed?term=%22Lindahl%20E%22%5BAuthor%5D , Hess B http://www.ncbi.nlm.nih.gov/pubmed?term=%22Hess%20B%22%5BAuthor%5D , Groenhof G http://www.ncbi.nlm.nih.gov/pubmed?term=%22Groenhof%20G%22%5BAuthor%5D , Mark AE http://www.ncbi.nlm.nih.gov/pubmed?term=%22Mark%20AE%22%5BAuthor%5D , Berendsen HJ http://www.ncbi.nlm.nih.gov/pubmed?term=%22Berendsen%20HJ%22%5BAuthor%5D . The performance there is around 1 ps/day. I do not understand why my speed is so slow and it seems that Ewald option makes it slow. The greatest performance obtained in the paper you quote uses virtual sites, long time steps, and plain cutoff (or RF) for electrostatics. Ewald summation methods are going to be slower. The system size will also be a major factor. The benchmarks are based on relatively small systems (10,000 atoms for the best- performing systems). If you have many more atoms, you can't expect the same performance. You're simply comparing apples to oranges. -Justin Thanks, Shuangxing Dai On Thu, Apr 15, 2010 at 10:18 AM, gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org mailto:gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org mailto:gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. slow speed (Shuangxing Dai) 2. Re: slow speed (Justin A. Lemkul) 3. Re: slow speed (XAvier Periole) 4. Re: slow speed (Mark Abraham) -- Message: 1 Date: Thu, 15 Apr 2010 10:02:47 -0400 From: Shuangxing Dai shuangxing...@gmail.com mailto:shuangxing...@gmail.com Subject: [gmx-users] slow speed To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: q2ka8381c791004150702ye4007304pa2156201ca4b5...@mail.gmail.com mailto:q2ka8381c791004150702ye4007304pa2156201ca4b5...@mail.gmail.com Content-Type: text/plain; charset=utf-8 Hi, gmx-users: I am using latest version of gromacs and found it was really slow. I was wondering anyone got the same experience and can point out where the problem is. I was running double precision for MD. But for each dynamics simulation, it takes 4 days. I should only take two or three hours. Here is the .mdp file: define = ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; 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 = 100 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 100 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 50 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 1 compressibility = 4.5e-05
[gmx-users] TIP3P water box
nbsp;Hello,Inbsp;want to nbsp;use spc216.gro and apply the tip3p.itp parameters, but it would make a mistake for the pre-processor grompp ,it said can't find HW atomtypes, the force file which I used is ffG43a1.itp. my tip3p.itp filenbsp;is as follows:nbsp; nbsp;[ moleculetype ] ; molnamenbsp;nrexcl SOLnbsp;nbsp;2 [ atoms ] ; idnbsp;at typenbsp;res nr nbsp;residu namenbsp;at namenbsp;nbsp;cg nrnbsp;charge #ifdef _FF_OPLS 1nbsp;nbsp;nbsp;nbsp; opls_111nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SOLnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; OWnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; -0.834 2nbsp;nbsp;nbsp;nbsp; opls_112nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SOLnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HW1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.417 3nbsp;nbsp;nbsp;nbsp; opls_112nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SOLnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HW2nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.417 #endif #ifdef _FF_CHARMM 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; OTnbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SOLnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; OWnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; -0.834 2nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HTnbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SOLnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HW1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.417 3nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HTnbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SOLnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HW2nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.417 #endif #ifdef _FF_GROMACS 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; OWT3nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SOLnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; OWnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; -0.834 2nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HWnbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SOLnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HW1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.417 3nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HWnbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SOLnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HW2nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.417 #endif #ifdef _FF_GROMOS96 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; OWT3nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SOLnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; OWnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; -0.834 2nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HWnbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SOLnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HW1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.417 3nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HWnbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SOLnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; HW2nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.417 #endif #ifdef FLEXIBLE [ bonds ] ; inbsp;jnbsp;functnbsp;lengthnbsp;force.c. 1nbsp;2nbsp;1nbsp;0.09572nbsp;502416.0 0.09572nbsp;502416.0 1nbsp;3nbsp;1nbsp;0.09572nbsp;502416.0 0.09572nbsp;502416.0 nbsp; [ angles ] ; inbsp;jnbsp;knbsp;functnbsp;anglenbsp;force.c. 2nbsp;1nbsp;3nbsp;1nbsp;104.52nbsp;628.02nbsp;104.52nbsp;628.02nbsp; #else [ settles ] ; inbsp;jnbsp;functnbsp;length 1nbsp;1nbsp;0.09572nbsp;0.15139 [ exclusions ] 1nbsp;2nbsp;3 2nbsp;1nbsp;3 3nbsp;1nbsp;2 #endif the version of the gromacs is 4.0.5. nbsp; Thank you for all your help ! nbsp;-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] TIP3P water box
If you get this to work, you may still have problems as SPC and TIP3P have different geometries. A box of 216 waters is pretty easy to equilibrate; you could have this done for TIP3P in no time at all. On Apr 16, 2010, at 4:46 AM, kecy...@sina.com wrote: Hello,I want to use spc216.gro and apply the tip3p.itp parameters, but it would make a mistake for the pre-processor grompp ,it said can't find HW atomtypes, the force file which I used is ffG43a1.itp. my tip3p.itp file is as follows: [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; id at type res nr residu name at name cg nr charge #ifdef _FF_OPLS 1 opls_111 1 SOL OW 1 -0.834 2 opls_112 1 SOL HW1 10.417 3 opls_112 1 SOL HW2 10.417 #endif #ifdef _FF_CHARMM 1 OT 1 SOL OW 1 -0.834 2 HT 1 SOL HW1 10.417 3 HT 1 SOL HW2 10.417 #endif #ifdef _FF_GROMACS 1 OWT31 SOL OW 1 -0.834 2 HW 1 SOL HW1 10.417 3 HW 1 SOL HW2 10.417 #endif #ifdef _FF_GROMOS96 1 OWT31 SOL OW 1 -0.834 2 HW 1 SOL HW1 10.417 3 HW 1 SOL HW2 10.417 #endif #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572 502416.0 1 3 1 0.09572 502416.0 0.09572 502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #else [ settles ] ; i j funct length 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif the version of the gromacs is 4.0.5. Thank you for all your help ! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Dihedral potentials
Hello, I have a question regarding the dihedral section in a topology file. If I define two parameters sets for the same dihedral, are the energies added up or is the first one replaced by the second one ? Unfortunately there is no sentence in the manual regarding this. Cheers, Flo -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert PGP.sig Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral potentials
On Apr 16, 2010, at 12:20 PM, Florian Dommert wrote: Hello, I have a question regarding the dihedral section in a topology file. If I define two parameters sets for the same dihedral, are the energies added up or is the first one replaced by the second one ? Unfortunately there is no sentence in the manual regarding this. Depends if you define it in the topology file or in the parameter file. In the topology file the sum would be used. In the parameter file I would think only one would be used ... no idea which but you could check this for a simple system and looking at the tpr file using gmxdump. XAvier Cheers, Flo -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Protein in water/DMSO mixture with Amber
Hi all, to say the truth I already sent a message regarding this subject some months ago, but since so much time has passed I thought I'd open a new thread, also because the situation has quite evolved. I'm trying to set up a simulation of a small (62 residues) protein in a mixture of water and DMSO with the AMBER99 forcefield. I found the parameters for such forcefield in the literature and used them to build a dmso.itp. Following yuor previous suggestions, I also obtained a dmso.gro file downloading a .sdf file from Pubchem and converting it to a .pdb and eventually to a .gro. Then I followed the mini-tutorial in the Gromacs site on simulations of mixed solvents: I added some DMSO molecules with genbox -ci -nmol and then filled the box with TIP3P water molecules. I also added 9 Cl- ions and, judging from what I could see with a visualization program, everything was fine. The problem came when I tried to run the energy minimization. I got the error: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) after only 5 minimization steps. I searched in the GROMACS site and in this mailing list as well to find out what the error meant and I read that this error can be sometimes ignored if the potential energy of the system is already low enough to run the simulation... but my Epot is 7.6367096e+16 . To be completely sure, I tried to run an MD simulation, but it immediately crashed with a water molecule cannot be settled error, which does not surprise me. What did I do wrong? Do I have to assume that there is something wrong in my dmso.itp file or in the way I ran the minimization? Thank you very much; I'm pasting my dmso.itp and em.mdp here. ###DMSO.ITP### [ moleculetype ] ; molname nrexcl DMSO2 [ atoms ] #ifdef _FF_AMBER99 ; nrtype resnr residue atomcgnrcharge mass 1 amber99_471 DMSOS 1 0.3155 32.06000 ; amber S type 2 amber99_411 DMSOO 1 -0.5205 16.0 ; amber O type 3 amber99_111 DMSOCT1 1 -0.3244 12.01000 ; amber C type 4 amber99_191 DMSOHT111 0.1423 1.00800 ; amber H type 5 amber99_191 DMSOHT12 1 0.1423 1.00800 ; amber H type 6 amber99_191 DMSOHT13 1 0.1423 1.00800 ; amber H type 7 amber99_111 DMSOCT2 1 -0.3244 12.01000 ; amber C type 8 amber99_191 DMSOHT211 0.1423 1.00800 ; amber H type 9 amber99_191 DMSOHT22 1 0.1423 1.00800 ; amber H type 10amber99_191 DMSOHT23 1 0.1423 1.00800 ; amber H type #endif [ bonds ] ; aiaj funct b0 kb 1 2 1 0.153 238602 1 3 1 0.181 95022 3 4 1 0.109 142324 3 5 1 0.109 142324 3 6 1 0.109 142324 1 7 1 0.181 95022 7 8 1 0.109 142324 7 9 1 0.109 142324 7 101 0.109 142324 [ angles ] ; aiajak functtheta kt 3 1 2 1106.75 334.88 3 1 7 197.40 259.53 2 1 7 1106.75 334.88 4 3 1 1109.50 209.30 6 3 1 1109.50 209.30 5 3 1 1109.50 209.30 5 3 4 1109.50 146.51 5 3 6 1109.50 146.51 4 3 6 1109.50 146.51 9 7 10 1109.50 146.51 8 7 9 1109.50 146.51 8 7 10 1109.50 146.51 9 7 1 1109.50 209.30 10 7 1 1109.50 209.30 8 7 1 1109.50 209.30 [ dihedrals ] ; ai aj ak al funct xi kxipn 2 1 3 6 1 1803.558 2 2 1 3 4 1 1803.558 2 2 1 3 5 1 1803.558 2 2 1 7 8 1 1803.558 2 2 1 7 9 1 1803.558 2 2 1 7 10 1 1803.558 2 3 1 7 8 1 1803.558 2 3 1 7 9 1 1803.558 2 3 1 7 10 1 1803.558 2 7 1 3
Re: [gmx-users] Protein in water/DMSO mixture with Amber
Simone Cirri wrote: Hi all, to say the truth I already sent a message regarding this subject some months ago, but since so much time has passed I thought I'd open a new thread, also because the situation has quite evolved. I'm trying to set up a simulation of a small (62 residues) protein in a mixture of water and DMSO with the AMBER99 forcefield. I found the parameters for such forcefield in the literature and used them to build a dmso.itp. Following yuor previous suggestions, I also obtained a dmso.gro file downloading a .sdf file from Pubchem and converting it to a .pdb and eventually to a .gro. Then I followed the mini-tutorial in the Gromacs site on simulations of mixed solvents: I added some DMSO molecules with genbox -ci -nmol and then filled the box with TIP3P water molecules. I also added 9 Cl- ions and, judging from what I could see with a visualization program, everything was fine. The problem came when I tried to run the energy minimization. I got the error: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) after only 5 minimization steps. I searched in the GROMACS site and in this mailing list as well to find out what the error meant and I read that this error can be sometimes ignored if the potential energy of the system is already low enough to run the simulation... but my Epot is 7.6367096e+16 . To be completely sure, I tried to run an MD simulation, but it immediately crashed with a water molecule cannot be settled error, which does not surprise me. What did I do wrong? Do I have to assume that there is something wrong in my dmso.itp file or in the way I ran the minimization? Thank you very much; I'm pasting my dmso.itp and em.mdp here. You could have some unresolvable atomic overlap in the system, so visual inspection is your friend there. You can also try using a larger value of emstep, something like 0.01, otherwise you could just be stuck in a high-energy region from which your structure won't escape using the tiny emstep you have set. -Justin ###DMSO.ITP### [ moleculetype ] ; molname nrexcl DMSO2 [ atoms ] #ifdef _FF_AMBER99 ; nrtype resnr residue atomcgnrcharge mass 1 amber99_471 DMSOS 1 0.3155 32.06000 ; amber S type 2 amber99_411 DMSOO 1 -0.5205 16.0 ; amber O type 3 amber99_111 DMSOCT1 1 -0.3244 12.01000 ; amber C type 4 amber99_191 DMSOHT111 0.1423 1.00800 ; amber H type 5 amber99_191 DMSOHT12 1 0.1423 1.00800 ; amber H type 6 amber99_191 DMSOHT13 1 0.1423 1.00800 ; amber H type 7 amber99_111 DMSOCT2 1 -0.3244 12.01000 ; amber C type 8 amber99_191 DMSOHT211 0.1423 1.00800 ; amber H type 9 amber99_191 DMSOHT22 1 0.1423 1.00800 ; amber H type 10amber99_191 DMSOHT23 1 0.1423 1.00800 ; amber H type #endif [ bonds ] ; aiaj funct b0 kb 1 2 1 0.153 238602 1 3 1 0.181 95022 3 4 1 0.109 142324 3 5 1 0.109 142324 3 6 1 0.109 142324 1 7 1 0.181 95022 7 8 1 0.109 142324 7 9 1 0.109 142324 7 101 0.109 142324 [ angles ] ; aiajak functtheta kt 3 1 2 1106.75 334.88 3 1 7 197.40 259.53 2 1 7 1106.75 334.88 4 3 1 1109.50 209.30 6 3 1 1109.50 209.30 5 3 1 1109.50 209.30 5 3 4 1109.50 146.51 5 3 6 1109.50 146.51 4 3 6 1109.50 146.51 9 7 10 1109.50 146.51 8 7 9 1109.50 146.51 8 7 10 1109.50 146.51 9 7 1 1109.50 209.30 10 7 1 1109.50 209.30 8 7 1 1109.50 209.30 [ dihedrals ] ; ai aj ak al funct xi kxipn 2 1 3 6 1 1803.558 2 2 1 3 4 1 1803.558 2 2 1 3 5 1 1803.558 2 2 1 7
Re: [gmx-users] Dihedral potentials
Hello Xavier, thank you very much for the quick reply. As I use it in the topol.top file everything is fine, so the dihedrals should add up. Cheers, Flo On 16.04.2010, at 15:05, XAvier Periole wrote: On Apr 16, 2010, at 12:20 PM, Florian Dommert wrote: Hello, I have a question regarding the dihedral section in a topology file. If I define two parameters sets for the same dihedral, are the energies added up or is the first one replaced by the second one ? Unfortunately there is no sentence in the manual regarding this. Depends if you define it in the topology file or in the parameter file. In the topology file the sum would be used. In the parameter file I would think only one would be used ... no idea which but you could check this for a simple system and looking at the tpr file using gmxdump. XAvier Cheers, Flo -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert PGP.sig Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral potentials
On Apr 16, 2010, at 3:22 PM, Florian Dommert wrote: Hello Xavier, thank you very much for the quick reply. As I use it in the topol.top file everything is fine, so the dihedrals should add up. yes, I noticed you actually mention it in your email :)) Cheers, Flo On 16.04.2010, at 15:05, XAvier Periole wrote: On Apr 16, 2010, at 12:20 PM, Florian Dommert wrote: Hello, I have a question regarding the dihedral section in a topology file. If I define two parameters sets for the same dihedral, are the energies added up or is the first one replaced by the second one ? Unfortunately there is no sentence in the manual regarding this. Depends if you define it in the topology file or in the parameter file. In the topology file the sum would be used. In the parameter file I would think only one would be used ... no idea which but you could check this for a simple system and looking at the tpr file using gmxdump. XAvier Cheers, Flo -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Dihedral potentials
Hi, In the dihedraltypes section (or any types section), redefining parameters for the same atom types generates a warning (saying it will use the last) and halts grompp, unless you use the -maxwarn option. For CHARMM there will be an exception to this rule in the next release. But I guess you don't mean defining parameters, but interactions in the [ dihedrals ] section. Any interactions listed there are added. If you add an interaction twice, you get double the potential (without warning). Berk From: domm...@icp.uni-stuttgart.de Date: Fri, 16 Apr 2010 12:20:11 +0200 To: gmx-users@gromacs.org Subject: [gmx-users] Dihedral potentials Hello, I have a question regarding the dihedral section in a topology file. If I define two parameters sets for the same dihedral, are the energies added up or is the first one replaced by the second one ? Unfortunately there is no sentence in the manual regarding this. Cheers, Flo --Florian DommertDipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Is PME related to nslist??
On 16/04/2010 10:47 AM, Joonho Lee wrote: Dear all, I am a little bit confused about electrostatic force calculation and need some clarification about PME. I normaly use PME for electrostatic force and rlist(=rcoulomb) is the parameter for real-space calculation. As you know, rlist is related NS and nstlist (the neighbor list update frequency). If I set nstlist=10, the neighbor list does not change between successive NS. The neighbour list changes at each step whose remainder after division by nstlist is zero. Q : In the real-space calculation procedure of PME, are the particles in the neighbor list only considered?? Yes. All particles that might be involved in non-bonded interactions are listed. If it is, when a new particle comes into the rlist, the PME calculation does not reflect the change until the next neighbor list update. Yep. Mark Thanks, Joon -- Joonho Lee Department of Mechanical Science and Engineering 3213 Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana, IL 61801 Email: lee...@uiuc.edu Phone: (217)778-9536 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Concerns with g_wham
Jennifer Casey wrote: Hello, I have been using g_wham, but I have a few questions that I can't find answers to online. When using WHAM, one does not need the forces between the pull groups to calculate the PMF, yet g_wham won't run without it. Is there a reason for this? Hi Jennifer! As pointed out by Chris, you can use provide the pull positions (g_wham -ix) OR the pull forces with -if. When giving the pullf files, g_wham simply computes the pull positions from the forces and calculates the histograms etc... Also, when using the pull code, I am allowed to define the spring constant K for umbrella sampling, but I do not designate where the umbrella potential is centered. How does gromacs determine this? Umbrella positions and force constants (and pull geometry) are taken from the tpr files. That's why they must be provided to g_wham. I am interested as I would like to create a PMF using umbrella integration (from code I will write myself) rather than use WHAM. To do this and still use the umbrella sampling runs used with GROMACS, I need to know where my umbrella potentials are centered. If you want to integrate the mean forces, I would not use pull=umbrella but pull=constraint. You should get the same PMF compared to umbrella sampling and using g_wham. Please let me know if g_wham makes any trouble. Cheers, Jochen Thank you, Jennifer -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] slow speed
nstlist = 50 ; ns algorithm (simple or grid) = ns_type = grid Oups, you are dong neighbor searching only every 50fs. Are you sure this is what you want? If you have a biological system this is probably not often enough. In biological systems people typically do neighbor searching every 10 to 20 fs. Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CG-MD simulation of protein, always crash with protein
On 15 Apr 2010, at 18:06, Trang wrote: My target system is a protein with lipid molecules added randomly (using GENBOX). Running MD, I expect to I hope you're using a larger van der Waals distance (0.24nm or so) when inserting the lipids. broke down the problem, that is, to run md simulation for the protein molecule only, and in vacuum. Still no improvement. Although all the distances in the minimized structure are visually proper, the system exploded. If you can't run the protein even in vacuum, then the problem is either in your MD parameters, starting co-ordinates or some simple mistake somewhere. Since the .mdp files you posted seem ok, my bet is on the starting co-ordinates, just as Xavier proposed. Could you post the system topology (.top) and the protein topology (.itp), so we can rule out any mistakes in those? You should also double check whether you have close contacts between some atoms in the protein; e.g. in VMD this is easily done using the dynamic bonds representation. -martti- -- Post-doctoral research fellow Moleculaire Dynamica University of Groningen Nijenborgh 4, 9747AG Groningen, the Netherlands tel. +(31) 50 363 4339 | fax. +(31) 50 363 4398 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] TIP3P water box
kecy...@sina.com wrote: Hello,I want to use spc216.gro and apply the tip3p.itp parameters, but it would make a mistake for the pre-processor grompp ,it said can't find HW atomtypes, the force file which I used is ffG43a1.itp. my tip3p.itp file is as follows: HW isn't a valid atom type for ffG43a1. See the .atp file for what is. What you probably want is H, not HW. -Justin /[ moleculetype ] ; molname nrexcl SOL 2/ /[ atoms ] ; id at type res nr residu name at name cg nr charge #ifdef _FF_OPLS 1 opls_111 1 SOL OW 1 -0.834 2 opls_112 1 SOL HW1 10.417 3 opls_112 1 SOL HW2 10.417 #endif #ifdef _FF_CHARMM 1 OT 1 SOL OW 1 -0.834 2 HT 1 SOL HW1 10.417 3 HT 1 SOL HW2 10.417 #endif #ifdef _FF_GROMACS 1 OWT31 SOL OW 1 -0.834 2 HW 1 SOL HW1 10.417 3 HW 1 SOL HW2 10.417 #endif #ifdef _FF_GROMOS96 1 OWT31 SOL OW 1 -0.834 2 HW 1 SOL HW1 10.417 3 HW 1 SOL HW2 10.417 #endif/ /#ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572 502416.0 1 3 1 0.09572 502416.0 0.09572 502416.0 / /[ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 / /#else [ settles ] ; i j funct length 1 1 0.09572 0.15139/ /[ exclusions ] 1 2 3 2 1 3 3 1 2 #endif/ the version of the gromacs is 4.0.5. Thank you for all your help ! -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] conversion of desmond trajectory files into gromacs
Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] conversion of desmond trajectory files into gromacs
VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Compiling Gromacs 4.0.7 on AIX 5.3
Hi Chris. Thank you for your answer I tried the 4.0.4 version but unfortunately, it did better but new errors appeared anyway so what I test now is another version of FFTW (fftw-2.1.5.tar.gz) and the make command for gromacs 4.0.7 was a success so the question is : What will be the difference in using Gromacs if I use FFTW2 instead of FFTW3 ? thanks again --- here are errors shown when compiling gromacs 4.0.7 with fftw 3.2.2 on AIX 5.3 --- cc -qlanglvl=extc89 -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\/usr/local/gromacs/share/top\ -I/usr/local/include -O3 -qarch=pwr5 -qtune=pwr5 -qmaxmem=16384 -c -M gmx_sdf.c -o gmx_sdf.o /usr/include/stdio.h, line 497.12: 1506-343 (S) Redeclaration of fgetpos64 differs from previous declaration on line 296 of /usr/include/stdio.h. /usr/include/stdio.h, line 497.12: 1506-377 (I) The type long long* of parameter 2 differs from the previous type long*. /usr/include/stdio.h, line 500.12: 1506-343 (S) Redeclaration of fseeko64 differs from previous declaration on line 440 of /usr/include/stdio.h. /usr/include/stdio.h, line 500.12: 1506-377 (I) The type long long of parameter 2 differs from the previous type long. /usr/include/stdio.h, line 501.12: 1506-343 (S) Redeclaration of fsetpos64 differs from previous declaration on line 298 of /usr/include/stdio.h. /usr/include/stdio.h, line 501.12: 1506-377 (I) The type const long long* of parameter 2 differs from the previous type const long*. /usr/include/stdio.h, line 502.16: 1506-343 (S) Redeclaration of ftello64 differs from previous declaration on line 441 of /usr/include/stdio.h. /usr/include/stdio.h, line 502.16: 1506-050 (I) Return type long long in redeclaration is not compatible with the previous return type long. /usr/include/unistd.h, line 171.17: 1506-343 (S) Redeclaration of lseek64 differs from previous declaration on line 169 of /usr/include/unistd.h. /usr/include/unistd.h, line 171.17: 1506-050 (I) Return type long long in redeclaration is not compatible with the previous return type long. /usr/include/unistd.h, line 171.17: 1506-377 (I) The type long long of parameter 2 differs from the previous type long. /usr/include/sys/lockf.h, line 64.20: 1506-343 (S) Redeclaration of lockf64 differs from previous declaration on line 62 of /usr/include/sys/lockf.h. /usr/include/sys/lockf.h, line 64.20: 1506-377 (I) The type long long of parameter 3 differs from the previous type long. /usr/include/unistd.h, line 800.33: 1506-343 (S) Redeclaration of ftruncate64 differs from previous declaration on line 798 of /usr/include/unistd.h. /usr/include/unistd.h, line 800.33: 1506-377 (I) The type long long of parameter 2 differs from the previous type long. /usr/include/unistd.h, line 836.33: 1506-343 (S) Redeclaration of truncate64 differs from previous declaration on line 834 of /usr/include/unistd.h. /usr/include/unistd.h, line 836.33: 1506-377 (I) The type long long of parameter 2 differs from the previous type long. /usr/include/unistd.h, line 853.33: 1506-343 (S) Redeclaration of pread64 differs from previous declaration on line 850 of /usr/include/unistd.h. /usr/include/unistd.h, line 853.33: 1506-377 (I) The type long long of parameter 4 differs from the previous type long. /usr/include/unistd.h, line 854.33: 1506-343 (S) Redeclaration of pwrite64 differs from previous declaration on line 851 of /usr/include/unistd.h. /usr/include/unistd.h, line 854.33: 1506-377 (I) The type long long of parameter 4 differs from the previous type long. /usr/include/unistd.h, line 921.25: 1506-343 (S) Redeclaration of fclear64 differs from previous declaration on line 918 of /usr/include/unistd.h. /usr/include/unistd.h, line 921.25: 1506-050 (I) Return type long long in redeclaration is not compatible with the previous return type long. /usr/include/unistd.h, line 921.25: 1506-377 (I) The type long long of parameter 2 differs from the previous type long. /usr/include/unistd.h, line 922.25: 1506-343 (S) Redeclaration of fsync_range64 differs from previous declaration on line 919 of /usr/include/unistd.h. /usr/include/unistd.h, line 922.25: 1506-377 (I) The type long long of parameter 3 differs from the previous type long. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 2. Stop. make: 1254-004 The error code from the last command is 1. Stop. Le 15/04/2010 19:38, chris.ne...@utoronto.ca a écrit : This worked for me on AIX 5.3 for gromacs 4.0.4, I didn't try to compile any gromacs versions after that because we found that gromacs runs much better on Xeons and Opterons than it runs on power6's running AIX 5.3 If you have a problem specific to 4.0.7 (i.e. you can compile 4.0.4 alright on AIX 5.3), then I'm sorry but I can not help you there. Note: be sure to modify the
Re: [gmx-users] conversion of desmond trajectory files into gromacs
Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl wrote: VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] conversion of desmond trajectory files into gromacs
Well I guess you want to use gmx analysis tools so you'll have to build the gmx topology of your system when necessary! Often only a pdb file or a gro file is sufficient. On Apr 16, 2010, at 5:24 PM, ram bio wrote: Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl wrote: VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] calculation of potential and Sg
Hello, I have a protein which has 4 Thr residues on its one side. I want to calculate the potential energy and Sg of water molecules these Thr residues are facing (up to 10 angstrom). I have a 10ns trajectory and I might need only 5ns of it. How should I set my index file and which tools will help me? Thanks in advance for your helps. Regards, Paymon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Compiling Gromacs 4.0.7 on AIX 5.3
Dear Sebastien: Perhaps it's obvious, but can you confirm that you used the compilation options that I posted? My suggestion was not so much that you should try to compile 4.0.4 but that you should try the options that I posted. So if you used your original compilation commands with gromacs version 4.0.4 then I am not surprised that it also failed to compile... please go back and attempt with the commands that I provided. If, however, you did try those options (and on v4.0.4) then I am sorry to say that I'm no expert at compilation -- a previous colleague worked out that AIX compillation for me and I'm just passing along what worked for me. Regarding the fftw question, I am sorry but that too I can not answer. Chris. -- original message -- Thank you for your answer I tried the 4.0.4 version but unfortunately, it did better but new errors appeared anyway so what I test now is another version of FFTW (fftw-2.1.5.tar.gz) and the make command for gromacs 4.0.7 was a success so the question is : What will be the difference in using Gromacs if I use FFTW2 instead of FFTW3 ? thanks again --- here are errors shown when compiling gromacs 4.0.7 with fftw 3.2.2 on AIX 5.3 --- cc -qlanglvl=extc89 -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\/usr/local/gromacs/share/top\ -I/usr/local/include -O3 -qarch=pwr5 -qtune=pwr5 -qmaxmem=16384 -c -M gmx_sdf.c -o gmx_sdf.o /usr/include/stdio.h, line 497.12: 1506-343 (S) Redeclaration of fgetpos64 differs from previous declaration on line 296 of /usr/include/stdio.h. /usr/include/stdio.h, line 497.12: 1506-377 (I) The type long long* of parameter 2 differs from the previous type long*. /usr/include/stdio.h, line 500.12: 1506-343 (S) Redeclaration of fseeko64 differs from previous declaration on line 440 of /usr/include/stdio.h. /usr/include/stdio.h, line 500.12: 1506-377 (I) The type long long of parameter 2 differs from the previous type long. /usr/include/stdio.h, line 501.12: 1506-343 (S) Redeclaration of fsetpos64 differs from previous declaration on line 298 of /usr/include/stdio.h. /usr/include/stdio.h, line 501.12: 1506-377 (I) The type const long long* of parameter 2 differs from the previous type const long*. /usr/include/stdio.h, line 502.16: 1506-343 (S) Redeclaration of ftello64 differs from previous declaration on line 441 of /usr/include/stdio.h. /usr/include/stdio.h, line 502.16: 1506-050 (I) Return type long long in redeclaration is not compatible with the previous return type long. /usr/include/unistd.h, line 171.17: 1506-343 (S) Redeclaration of lseek64 differs from previous declaration on line 169 of /usr/include/unistd.h. /usr/include/unistd.h, line 171.17: 1506-050 (I) Return type long long in redeclaration is not compatible with the previous return type long. /usr/include/unistd.h, line 171.17: 1506-377 (I) The type long long of parameter 2 differs from the previous type long. /usr/include/sys/lockf.h, line 64.20: 1506-343 (S) Redeclaration of lockf64 differs from previous declaration on line 62 of /usr/include/sys/lockf.h. /usr/include/sys/lockf.h, line 64.20: 1506-377 (I) The type long long of parameter 3 differs from the previous type long. /usr/include/unistd.h, line 800.33: 1506-343 (S) Redeclaration of ftruncate64 differs from previous declaration on line 798 of /usr/include/unistd.h. /usr/include/unistd.h, line 800.33: 1506-377 (I) The type long long of parameter 2 differs from the previous type long. /usr/include/unistd.h, line 836.33: 1506-343 (S) Redeclaration of truncate64 differs from previous declaration on line 834 of /usr/include/unistd.h. /usr/include/unistd.h, line 836.33: 1506-377 (I) The type long long of parameter 2 differs from the previous type long. /usr/include/unistd.h, line 853.33: 1506-343 (S) Redeclaration of pread64 differs from previous declaration on line 850 of /usr/include/unistd.h. /usr/include/unistd.h, line 853.33: 1506-377 (I) The type long long of parameter 4 differs from the previous type long. /usr/include/unistd.h, line 854.33: 1506-343 (S) Redeclaration of pwrite64 differs from previous declaration on line 851 of /usr/include/unistd.h. /usr/include/unistd.h, line 854.33: 1506-377 (I) The type long long of parameter 4 differs from the previous type long. /usr/include/unistd.h, line 921.25: 1506-343 (S) Redeclaration of fclear64 differs from previous declaration on line 918 of /usr/include/unistd.h. /usr/include/unistd.h, line 921.25: 1506-050 (I) Return type long long in redeclaration is not compatible with the previous return type long. /usr/include/unistd.h, line 921.25: 1506-377 (I) The type long long of parameter 2 differs from the previous type long. /usr/include/unistd.h, line 922.25: 1506-343 (S) Redeclaration of fsync_range64 differs from previous declaration on line 919 of /usr/include/unistd.h. /usr/include/unistd.h, line 922.25: 1506-377 (I) The type long long of parameter 3 differs from the previous type long.
Re: [gmx-users] conversion of desmond trajectory files into gromacs
In case you use the GIT version of the analysis tools you don't need to convert the trajectories first. I've added that the analysis tools can read all vmd supported file formats if GROMACS finds the vmd libraries. Roland On Fri, Apr 16, 2010 at 11:33 AM, XAvier Periole x.peri...@rug.nl wrote: Well I guess you want to use gmx analysis tools so you'll have to build the gmx topology of your system when necessary! Often only a pdb file or a gro file is sufficient. On Apr 16, 2010, at 5:24 PM, ram bio wrote: Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl wrote: VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] load imbalance
Hi All! i have been getting this messsage in my log file. Started mdrun on node 0 Tue Apr 13 14:28:28 2010 Step Time Lambda 00.00.0 Energies (kJ/mol) Angle G96AngleProper Dih. Improper Dih. LJ-14 3.63316e+042.60311e+032.05878e+038.63051e+02 -4.53144e+01 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) Coul. recip. 5.46208e+042.42763e+05 -4.16328e+03 -1.65989e+06 -2.39317e+05 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -1.56418e+062.63757e+05 -1.30042e+063.00341e+02 -4.19843e+03 Cons. rmsd () 9.18296e-06 DD step 9 load imb.: force 1.3% DD step 9 load imb.: force 2.1% Step Time Lambda 10 200.20.0 IT IS SOME THING TO DO WITH IMBALANCE. and the force increases with time! I have a few questions based on this above report in my log file 1. Is this some serious problem? 2. Can I ignore this and proceed or do some thing to rectify the problem, if so please tell me what? I am using gromacs 4.0.5 and using 4 nodes, Any help would be appreciated. Thank you Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] load imbalance
jayant james wrote: Hi All! i have been getting this messsage in my log file. Started mdrun on node 0 Tue Apr 13 14:28:28 2010 Step Time Lambda 00.00.0 Energies (kJ/mol) Angle G96AngleProper Dih. Improper Dih. LJ-14 3.63316e+042.60311e+032.05878e+038.63051e+02 -4.53144e+01 Coulomb-14LJ (SR)LJ (LR) Coulomb (SR) Coul. recip. 5.46208e+042.42763e+05 -4.16328e+03 -1.65989e+06 -2.39317e+05 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -1.56418e+062.63757e+05 -1.30042e+063.00341e+02 -4.19843e+03 Cons. rmsd () 9.18296e-06 DD step 9 load imb.: force 1.3% DD step 9 load imb.: force 2.1% Step Time Lambda 10 200.20.0 IT IS SOME THING TO DO WITH IMBALANCE. and the force increases with time! I have a few questions based on this above report in my log file 1. Is this some serious problem? 2. Can I ignore this and proceed or do some thing to rectify the problem, if so please tell me what? Please read the manual, section 3.17.2, which explains dynamic load balancing, what the output is, and what it means. Of particular interest is the second paragraph on page 43. -Justin I am using gromacs 4.0.5 and using 4 nodes, Any help would be appreciated. Thank you Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp http://www.chick.com/reading/tracts/0096/0096_01.asp) -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS reproducibility
Hi. I am modelling a putative interaction between two proteins by doing MD of the docked complex with GROMACS 4.0. But each time I run the MD simulating 200 ps, the evolves in a different manner, and the average coordinates are different in a loop believed to help to the interaction. When I plot the LJ and coulumb energies between the two proteins, they are two different. ¿Is it reasonable to select the simulation that gives the better energies and moves the interaction loop towards the interaction partner, and continue with these simulation for ~2 nanoseconds? ¿or I have to do further analysis?. Sincerely yours. Lucio. -- Lucio Ricardo Montero Valenzuela Estudiante de doctorado en Ciencias Bioquímicas Lab. del Dr. Federico Sánchez Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS reproducibility
Lucio Ricardo Montero Valenzuela wrote: Hi. I am modelling a putative interaction between two proteins by doing MD of the docked complex with GROMACS 4.0. But each time I run the MD simulating 200 ps, the evolves in a different manner, and the average coordinates are different in a loop believed to help to the interaction. When I plot the LJ and coulumb energies between the two proteins, they are two different. ¿Is it reasonable to select the simulation that gives the better energies and moves the interaction loop towards the interaction partner, and continue with these simulation for ~2 nanoseconds? ¿or I have to do further analysis?. I suppose that depends on your intent. Are you trying to reproduce experimentally-determined interactions that you know should occur? Or do you have some other purpose? In any case, you can't expect every simulation to do exactly the same thing. Only over long time periods will independent simulations converge in their observable properties. Depending on the size of the loop and nature of the interactions between your proteins, 2 ns may not be enough. Likely it is not, and given the speed of Gromacs 4, there is no reason that tens of ns can't be done in a reasonably short period of time. -Justin Sincerely yours. Lucio. -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to use the walls
Hello, I had posted this message yesterday,maybe it was missing.I want to use the wall for 2d periodic boundary, but I don't know how to set the wall_type and wall_density, I don't know what thay depend on for setting. I also want to know the format of them for setting. nbsp; Thank you !-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
