Re: [gmx-users] Re: grompp for minimization: note warning
Hi Shahab, What did you do exactly? Can you state your complete protocol (1. fetched this structure file there, 2. got the topology from there, 3. did something, 4. ran grompp like this, etc)? Use brief, clear explanations and the command lines as you issued them. Cheers, Tsjerk On Tue, Sep 17, 2013 at 2:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/17/13 8:47 AM, shahab shariati wrote: Dear Justin Very very thanks for your quick reply. I am very confused and amazed. After visualization of atom 618 ( where the maximum force is), what should I do to resolve me problem. Any help will highly appreciated. I honestly have no idea. There's something nasty going on there, but only you have the ability to see it. You can always try a smaller value of emstep, a different EM algorithm, etc. Try setting nstxout = 1 and visualize the entire EM trajectory to see where things start to go out of control. And finally, if it really isn't working, ask the people who provided the coordinates - they're supposed to be pre-equilibrated, so if you can't get it to minimize, maybe there's something wrong that's happened before you even got your hands on the file. -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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- 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] Re: grompp for minimization: note warning
Dear Tsjerk Thanks for your consideration. My system contains 2 components: (DOPC cholesterol) lipids + water molecules. I get force field parameters from lipid book (for dopc and cholesterol). I used input coordinate file (system.gro) from following web site: http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html em.mdp file is as follows: - ; em.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions - For doing minimization, I used following command: grompp -f em.mdp -c system.gro -p topol.top -o em.tpr and then I get following result: - WARNING 1 [file topol.top, line 32]: 3632 non-matching atom names atom names from topol.top will be used atom names from system.gro will be ignored Analysing residue names: Warning: file does not end with a newline, last line: IB+ Ion There are: 128 Other residues There are: 1706 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 29019.00 Largest charge group radii for Van der Waals: 1.541, 1.514 nm Largest charge group radii for Coulomb: 0.079, 0.079 nm WARNING 2 [file em.mdp]: The sum of the two largest charge group radii (3.054313) is larger than rlist (1.20) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x72x72, spacing 0.111 0.120 0.116 Estimate for the relative computational load of the PME mesh part: 0.62 NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 133 Mb of data There was 1 note There were 2 warnings - I used -maxwarn option and I obtained em.tpr file. Then, for doing minimization, I used following command: mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log and then I get following result: - Reading file em.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Making 2D domain decomposition 1 x 2 x 2 Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 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) writing lowest energy coordinates. Steepest Descents converged to machine precision in 881 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.1828770e+05 Maximum force = 1.3656898e+04 on atom 618 Norm of force = 5.1748779e+02 - When I see created gro file (em.gro) by VMD, some dopc or cholesterol molecules are broken to 2 or 3 parts. I tested different ways: 1) change of parameters in em.mdp file ( emstep, nstep, EM algorithm ) 2) change of box size 3) I used the newest version of gromacs (4.6.3) But, unfortunatele, my problem was not solved. Certainly, I can not use this structure for next step (equilibration). How to solve this problem. Any help will highly appreciated. Best wishes for 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/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.
Re: [gmx-users] Re: grompp for minimization: note warning
Hi Shahab, That site has a lot of structures. It would be better to explicitly state which one you took. However, in this case, the better question is, how did you write the topology, and did you check the correspondence of the order of molecules/atoms in the topology file and the structure file? I guess the answer to the latter is no... - WARNING 1 [file topol.top, line 32]: 3632 non-matching atom names atom names from topol.top will be used atom names from system.gro will be ignored Never ignore this warning, unless you understand why this is okay. Cheers, Tsjerk -- 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] periodic molecule
Hello! I have a surface, formed by Mg2Al(OH)6. All of the O are bonded with Al, by such forming a mesh. I am using periodic_molecule=yes as discussed in this thread: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-td5010192.html#a5010234 I set up the topology for the small unit shown in blue frame on this picture - http://gromacs.5086.x6.nabble.com/file/n5010233/Screen_Shot_2013-07-31_at_13.41.17.png Then I make a big layered structure of 4 x 4 x 4 of such units and do energy minimisation, using following script: integrator = steep nsteps = 5000 emtol= 10 emstep = 0.01 nstxout = 1 nstenergy= 1 rlist= 1.0 pbc = xyz periodic_molecules = yes coulombtype = PME rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 And my Al that had bonds across periodic system (al2 and al3) move - see movie: https://docs.google.com/file/d/0B6Qm4snFANimRXZ3QTlVQ1J0MlE/edit?usp=sharing Colour coding: al2 is shown as large cyan and al3 is shown as large blue. al1 is shown in small cyan - it's the only al that does not do a big move. all mg are shown in pink I am not sure - have I set up periodic molecule wrong? My molecule.rtp for the using looks like: [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 0 0 [ B21 ] ;# ldh21 [ atoms ] ; atomname atomtype charge chargegroup o1 oc18 -0.875 3 h1 hoy0.350 3 o2 oc17 -0.875 3 h2 hoy0.350 3 o3 oc20 -0.875 3 h3 hoy0.350 3 o4 oc21 -0.875 1 h4 hoy0.350 1 o5 oc16 -0.875 1 h5 hoy0.350 1 o6 oc19 -0.875 1 h6 hoy0.350 1 mg1 mg1.400 al1 ac3 1.351 mg2 mg1.400 o7 oc16 -0.875 2 h7 hoy0.350 2 o8 oc19 -0.875 2 h8 hoy0.350 2 o9 oc18 -0.875 1 h9 hoy0.350 1 o10 oc17 -0.875 1 h10 hoy0.350 1 o11 oc20 -0.875 1 h11 hoy0.350 1 o12 oc21 -0.875 2 h12 hoy0.350 2 mg3 mg1.400 mg4 mg1.400 al2 ac3 1.352 o13 oc20 -0.875 2 h13 hoy0.350 2 o14 oc21 -0.875 3 h14 hoy0.350 3 o15 oc16 -0.875 3 h15 hoy0.350 3 o16 oc19 -0.875 3 h16 hoy0.350 3 o17 oc18 -0.875 2 h17 hoy0.350 2 o18 oc17 -0.875 2 h18 hoy0.350 2 al3 ac3 1.353 mg5 mg1.400 mg6 mg1.400 [ bonds ] ; atom1 atom2 parametersindex o1 h1 b_oc-h o2 h2 b_oc-h o3 h3 b_oc-h o4 h4 b_oc-h o5 h5 b_oc-h o6 h6 b_oc-h o7 h7 b_oc-h o8 h8 b_oc-h o9 h9 b_oc-h o10 h10 b_oc-h o11 h11 b_oc-h o12 h12 b_oc-h o13 h13 b_oc-h o14 h14 b_oc-h o15 h15 b_oc-h o16 h16 b_oc-h o17 h17 b_oc-h o18 h18 b_oc-h o1 al3 b_ac-oc o2 al3 b_ac-oc o3 al3 b_ac-oc o4 al1 b_ac-oc o5 al1 b_ac-oc o6 al1 b_ac-oc o7 al2 b_ac-oc o8 al2 b_ac-oc o9 al1 b_ac-oc o10 al1 b_ac-oc o11 al1 b_ac-oc o12 al2 b_ac-oc o13 al2 b_ac-oc o14 al3 b_ac-oc o15 al3 b_ac-oc o16 al3 b_ac-oc o17 al2 b_ac-oc o18 al2 b_ac-oc [ angles ] ; aiajak gromos type al3 o14 h14 a_ac-oc-h al3 o15 h15 a_ac-oc-h al3 o1 h1 a_ac-oc-h al3 o16 h16 a_ac-oc-h al3 o2 h2 a_ac-oc-h al3 o3 h3 a_ac-oc-h al1 o4 h4 a_ac-oc-h al1 o5 h5 a_ac-oc-h al1 o9 h9 a_ac-oc-h al1 o6 h6 a_ac-oc-h al1 o10 h10 a_ac-oc-h al1 o11 h11 a_ac-oc-h al2 o12 h12 a_ac-oc-h al2 o7 h7 a_ac-oc-h al2 o17 h17 a_ac-oc-h al2 o8 h8 a_ac-oc-h al2 o18 h18 a_ac-oc-h al2 o13 h13 a_ac-oc-h o5 al1 o10 a_oc-ac-oc_1 o7 al2 o18 a_oc-ac-oc_1 o15 al3 o2 a_oc-ac-oc_1 o9 al1 o6 a_oc-ac-oc_1 o17 al2 o8 a_oc-ac-oc_1 o1 al3 o16 a_oc-ac-oc_1 o11 al1 o4 a_oc-ac-oc_1 o13 al2 o12 a_oc-ac-oc_1 o3 al3 o14 a_oc-ac-oc_1 o5 al1 o9 a_oc-ac-oc_2 o7 al2 o17 a_oc-ac-oc_2 o15 al3 o1 a_oc-ac-oc_2 o5 al1 o4 a_oc-ac-oc_2 o7 al2 o12 a_oc-ac-oc_2 o15 al3 o14 a_oc-ac-oc_2 o10 al1 o6 a_oc-ac-oc_2 o18 al2 o8 a_oc-ac-oc_2 o2 al3 o16 a_oc-ac-oc_2 o10 al1 o11 a_oc-ac-oc_2 o18 al2 o13 a_oc-ac-oc_2 o2 al3 o3 a_oc-ac-oc_2 o9 al1 o4 a_oc-ac-oc_2 o17 al2 o12 a_oc-ac-oc_2 o1 al3 o14 a_oc-ac-oc_2 o6 al1 o11 a_oc-ac-oc_2 o8 al2 o13 a_oc-ac-oc_2 o16 al3 o3 a_oc-ac-oc_2 o5 al1 o6 a_oc-ac-oc_3 o7 al2 o8 a_oc-ac-oc_3 o15 al3 o16 a_oc-ac-oc_3 o5 al1 o11
[gmx-users] SHAKE or LINCS for free energy computations.
Hi everybody! I have a question about free energy computation. What algorithm i should use for constraining h-bonds SHAKE or LINCS then i'm doing free energy computation? Is any sufficient difference is exist? Sergey. -- View this message in context: http://gromacs.5086.x6.nabble.com/SHAKE-or-LINCS-for-free-energy-computations-tp5011272.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] periodic molecule
On 9/18/13 5:42 AM, Valentina wrote: Hello! I have a surface, formed by Mg2Al(OH)6. All of the O are bonded with Al, by such forming a mesh. I am using periodic_molecule=yes as discussed in this thread: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-td5010192.html#a5010234 I set up the topology for the small unit shown in blue frame on this picture - http://gromacs.5086.x6.nabble.com/file/n5010233/Screen_Shot_2013-07-31_at_13.41.17.png Then I make a big layered structure of 4 x 4 x 4 of such units and do energy minimisation, using following script: integrator = steep nsteps = 5000 emtol= 10 emstep = 0.01 nstxout = 1 nstenergy= 1 rlist= 1.0 pbc = xyz periodic_molecules = yes coulombtype = PME rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 And my Al that had bonds across periodic system (al2 and al3) move - see movie: https://docs.google.com/file/d/0B6Qm4snFANimRXZ3QTlVQ1J0MlE/edit?usp=sharing Colour coding: al2 is shown as large cyan and al3 is shown as large blue. al1 is shown in small cyan - it's the only al that does not do a big move. all mg are shown in pink I am not sure - have I set up periodic molecule wrong? My molecule.rtp for the using looks like: [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 0 0 [ B21 ] ;# ldh21 [ atoms ] ; atomname atomtype charge chargegroup o1 oc18 -0.875 3 h1 hoy0.350 3 o2 oc17 -0.875 3 h2 hoy0.350 3 o3 oc20 -0.875 3 h3 hoy0.350 3 o4 oc21 -0.875 1 h4 hoy0.350 1 o5 oc16 -0.875 1 h5 hoy0.350 1 o6 oc19 -0.875 1 h6 hoy0.350 1 mg1 mg1.400 al1 ac3 1.351 mg2 mg1.400 o7 oc16 -0.875 2 h7 hoy0.350 2 o8 oc19 -0.875 2 h8 hoy0.350 2 o9 oc18 -0.875 1 h9 hoy0.350 1 o10 oc17 -0.875 1 h10 hoy0.350 1 o11 oc20 -0.875 1 h11 hoy0.350 1 o12 oc21 -0.875 2 h12 hoy0.350 2 mg3 mg1.400 mg4 mg1.400 al2 ac3 1.352 o13 oc20 -0.875 2 h13 hoy0.350 2 o14 oc21 -0.875 3 h14 hoy0.350 3 o15 oc16 -0.875 3 h15 hoy0.350 3 o16 oc19 -0.875 3 h16 hoy0.350 3 o17 oc18 -0.875 2 h17 hoy0.350 2 o18 oc17 -0.875 2 h18 hoy0.350 2 al3 ac3 1.353 mg5 mg1.400 mg6 mg1.400 [ bonds ] ; atom1 atom2 parametersindex o1 h1 b_oc-h o2 h2 b_oc-h o3 h3 b_oc-h o4 h4 b_oc-h o5 h5 b_oc-h o6 h6 b_oc-h o7 h7 b_oc-h o8 h8 b_oc-h o9 h9 b_oc-h o10 h10 b_oc-h o11 h11 b_oc-h o12 h12 b_oc-h o13 h13 b_oc-h o14 h14 b_oc-h o15 h15 b_oc-h o16 h16 b_oc-h o17 h17 b_oc-h o18 h18 b_oc-h o1 al3 b_ac-oc o2 al3 b_ac-oc o3 al3 b_ac-oc o4 al1 b_ac-oc o5 al1 b_ac-oc o6 al1 b_ac-oc o7 al2 b_ac-oc o8 al2 b_ac-oc o9 al1 b_ac-oc o10 al1 b_ac-oc o11 al1 b_ac-oc o12 al2 b_ac-oc o13 al2 b_ac-oc o14 al3 b_ac-oc o15 al3 b_ac-oc o16 al3 b_ac-oc o17 al2 b_ac-oc o18 al2 b_ac-oc [ angles ] ; aiajak gromos type al3 o14 h14 a_ac-oc-h al3 o15 h15 a_ac-oc-h al3 o1 h1 a_ac-oc-h al3 o16 h16 a_ac-oc-h al3 o2 h2 a_ac-oc-h al3 o3 h3 a_ac-oc-h al1 o4 h4 a_ac-oc-h al1 o5 h5 a_ac-oc-h al1 o9 h9 a_ac-oc-h al1 o6 h6 a_ac-oc-h al1 o10 h10 a_ac-oc-h al1 o11 h11 a_ac-oc-h al2 o12 h12 a_ac-oc-h al2 o7 h7 a_ac-oc-h al2 o17 h17 a_ac-oc-h al2 o8 h8 a_ac-oc-h al2 o18 h18 a_ac-oc-h al2 o13 h13 a_ac-oc-h o5 al1 o10 a_oc-ac-oc_1 o7 al2 o18 a_oc-ac-oc_1 o15 al3 o2 a_oc-ac-oc_1 o9 al1 o6 a_oc-ac-oc_1 o17 al2 o8 a_oc-ac-oc_1 o1 al3 o16 a_oc-ac-oc_1 o11 al1 o4 a_oc-ac-oc_1 o13 al2 o12 a_oc-ac-oc_1 o3 al3 o14 a_oc-ac-oc_1 o5 al1 o9 a_oc-ac-oc_2 o7 al2 o17 a_oc-ac-oc_2 o15 al3 o1 a_oc-ac-oc_2 o5 al1 o4 a_oc-ac-oc_2 o7 al2 o12 a_oc-ac-oc_2 o15 al3 o14 a_oc-ac-oc_2 o10 al1 o6 a_oc-ac-oc_2 o18 al2 o8 a_oc-ac-oc_2 o2 al3 o16 a_oc-ac-oc_2 o10 al1 o11 a_oc-ac-oc_2 o18 al2 o13 a_oc-ac-oc_2 o2 al3 o3 a_oc-ac-oc_2 o9 al1 o4 a_oc-ac-oc_2 o17 al2 o12 a_oc-ac-oc_2 o1 al3 o14 a_oc-ac-oc_2 o6 al1 o11 a_oc-ac-oc_2 o8 al2 o13 a_oc-ac-oc_2 o16 al3 o3 a_oc-ac-oc_2 o5 al1
[gmx-users] Re: Why do you delete the messages?
You mean this one? http://gromacs.5086.x6.nabble.com/The-computational-methods-used-in-Gromacs-td5011269.html you have posted it in Gromacs general forum, but checking for it in Gromacs Users forum (i.e sub-forum) hence don't see it! V -- View this message in context: http://gromacs.5086.x6.nabble.com/Why-do-you-delete-the-messages-tp5011273p5011275.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] Re: periodic molecule
Thank you! Yep, they seem to be wanting to bond to the O's within the cell, while they are meant to bond across the PBC. I am not sure how periodic_molecule = yes part functions. I don't seem to get difference if I turn it on or off when I do Energy minimisation. Do you have some examples that work, so I can compare to them? Are there some threshold distances, that they rely upon? I really wouldn't like to have to make the a bigger basic cell - too much topology assigning. Thanks, V -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011277.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: periodic molecule
On 9/18/13 8:07 AM, Valentina wrote: Thank you! Yep, they seem to be wanting to bond to the O's within the cell, while they are meant to bond across the PBC. I am not sure how periodic_molecule = yes part functions. I don't seem to get difference if I turn it on or off when I do Energy minimisation. Do you have some examples that work, so I can compare to them? Are there some I have never used periodic molecules, except when toying around with some CNTs for my own curiosity. I suspect the problem you're seeing arises from the bonded atoms being closer within the unit cell than they are across PBC, so the minimum distance is what is trying to be satisfied. How far apart are the atoms across PBC, and how long is the assigned bond supposed to be? I have seen other cases posted to the list wherein the periodic_molecules function breaks down simply because of bad starting geometry. threshold distances, that they rely upon? I really wouldn't like to have to make the a bigger basic cell - too much topology assigning. A bigger unit cell won't help. In fact, it would probably make things worse. -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] Re: periodic molecule
Justin Lemkul wrote On 9/18/13 8:07 AM, Valentina wrote: Thank you! Yep, they seem to be wanting to bond to the O's within the cell, while they are meant to bond across the PBC. I am not sure how periodic_molecule = yes part functions. I don't seem to get difference if I turn it on or off when I do Energy minimisation. Do you have some examples that work, so I can compare to them? Are there some I have never used periodic molecules, except when toying around with some CNTs for my own curiosity. I suspect the problem you're seeing arises from the bonded atoms being closer within the unit cell than they are across PBC, so the minimum distance is what is trying to be satisfied. Nope, thats not the case. Across pbc it's 2.06A while across the cell it's 7.89A (see the attached pic, where in bold are the atoms whitin the cell and small are the periodic representation it should bond to) http://gromacs.5086.x6.nabble.com/file/n5011279/Screen_Shot_2013-09-18_at_13.30.23.png How far apart are the atoms across PBC, and how long is the assigned bond supposed to be? I have seen other cases posted to the list wherein the periodic_molecules function breaks down simply because of bad starting geometry. threshold distances, that they rely upon? I really wouldn't like to have to make the a bigger basic cell - too much topology assigning. A bigger unit cell won't help. In fact, it would probably make things worse. Agree, thank you! -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 jalemkul@.umaryland | (410) 706-7441 == -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011279.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] Help g_energy
Hello. I was calculating the viscosity of hexane through the Gromacs command g_energy. Three files are generated: visco.xvg, evisco.xvg and eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but the value does not match the experimental. I used 8 ns simulation at equilibrium. However, the file evisco.xvg has a value very close to the experimental but has only a time of 2 ns (version 4.0.7). I want to know what is present in the file eviscoi.xvg. Thank you. http://help-gromacs.blogspot.com.br/2013/09/viscosidade-gromacs-407.html -- 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: periodic molecule
On 9/18/13 8:34 AM, Valentina wrote: Justin Lemkul wrote On 9/18/13 8:07 AM, Valentina wrote: Thank you! Yep, they seem to be wanting to bond to the O's within the cell, while they are meant to bond across the PBC. I am not sure how periodic_molecule = yes part functions. I don't seem to get difference if I turn it on or off when I do Energy minimisation. Do you have some examples that work, so I can compare to them? Are there some I have never used periodic molecules, except when toying around with some CNTs for my own curiosity. I suspect the problem you're seeing arises from the bonded atoms being closer within the unit cell than they are across PBC, so the minimum distance is what is trying to be satisfied. Nope, thats not the case. Across pbc it's 2.06A while across the cell it's 7.89A (see the attached pic, where in bold are the atoms whitin the cell and small are the periodic representation it should bond to) http://gromacs.5086.x6.nabble.com/file/n5011279/Screen_Shot_2013-09-18_at_13.30.23.png How far apart are the atoms across PBC, and how long is the assigned bond supposed to be? I have seen other cases posted to the list wherein the periodic_molecules function breaks down simply because of bad starting geometry. Can you please address this question regarding the desired bond length, as well? If the distance is not within the normal tolerance (10%), then a bond will not be detected across PBC and thus will default to forming within the unit cell. -Justin threshold distances, that they rely upon? I really wouldn't like to have to make the a bigger basic cell - too much topology assigning. A bigger unit cell won't help. In fact, it would probably make things worse. Agree, thank you! -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 jalemkul@.umaryland | (410) 706-7441 == -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011279.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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] Error while simulating Protein in SDS/Water
Dear GMX users, I am trying to simulate a protein in SDS/Water box. 1. No problems with pdb2gmx - .gro file and .top files were generated. /pdb2gmx -f protein.pdb -o protein_pro.gro -water spce/ selected ff 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 2. Created a Cubic box using editconf /editconf -f protein_pro.gro -o protein_newbox.gro -c -d 1.0 -bt cubic/ 3. Then solvated the system using genbox genbox -cp protein_newbox.gro -cs spc216.gro -ci sds.gro -nmol 215 -o protein_solv.gro -p topol.top 4. After this step I looked at the topol.top file and I found that it was not fully updated and so I manually updated by adding no. of SDS molecules under [ molecules ] section at the very end. Also I added #include sds.itp whereever it was required. In fact I followed the discussion between Justin, Mark and Anna Marabotti at the following link: http://lists.gromacs.org/pipermail/gmx-users/2009-June/042704.html and did everything that was suggested. 5. When I use grompp after the step 4 grompp -f minim.mdp -c protein_solv.gro -p topol.top -o protein.tpr This is where I am getting a Fatal Error saying that the number of Co-ordinates in protein_solv.gro do not match with the number of co-ordinates in topol.top. Could you please help regarding this... Please give me your valuable suggestions. With Thanks and Best Regards Naresh -- View this message in context: http://gromacs.5086.x6.nabble.com/Error-while-simulating-Protein-in-SDS-Water-tp5011282.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] Error while simulating Protein in SDS/Water
Look at the numbers, count the number of atoms you expect in each moleculetype, and work out what the mismatch is. Mark On Wed, Sep 18, 2013 at 2:58 PM, naresh_sssihl knnar...@sssihl.edu.in wrote: Dear GMX users, I am trying to simulate a protein in SDS/Water box. 1. No problems with pdb2gmx - .gro file and .top files were generated. /pdb2gmx -f protein.pdb -o protein_pro.gro -water spce/ selected ff 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 2. Created a Cubic box using editconf /editconf -f protein_pro.gro -o protein_newbox.gro -c -d 1.0 -bt cubic/ 3. Then solvated the system using genbox genbox -cp protein_newbox.gro -cs spc216.gro -ci sds.gro -nmol 215 -o protein_solv.gro -p topol.top 4. After this step I looked at the topol.top file and I found that it was not fully updated and so I manually updated by adding no. of SDS molecules under [ molecules ] section at the very end. Also I added #include sds.itp whereever it was required. In fact I followed the discussion between Justin, Mark and Anna Marabotti at the following link: http://lists.gromacs.org/pipermail/gmx-users/2009-June/042704.html and did everything that was suggested. 5. When I use grompp after the step 4 grompp -f minim.mdp -c protein_solv.gro -p topol.top -o protein.tpr This is where I am getting a Fatal Error saying that the number of Co-ordinates in protein_solv.gro do not match with the number of co-ordinates in topol.top. Could you please help regarding this... Please give me your valuable suggestions. With Thanks and Best Regards Naresh -- View this message in context: http://gromacs.5086.x6.nabble.com/Error-while-simulating-Protein-in-SDS-Water-tp5011282.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 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: periodic molecule
Thank you, Yes. The bond between Al and O is 1.96 A So it should be within 10% from 2.06 A, so the lowest size is 1.854 A? It should be able to pick up 1.96 A then. Am I right? -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011284.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: periodic molecule
On 9/18/13 9:09 AM, Valentina wrote: Thank you, Yes. The bond between Al and O is 1.96 A So it should be within 10% from 2.06 A, so the lowest size is 1.854 A? It should be able to pick up 1.96 A then. Am I right? In theory, that bond should work. It looks like a pretty complex system though, so any number of things could be breaking. Are your bonds constrained, or simple harmonic interactions? If the latter, there is no guarantee that you can preserve the original geometry. Check the inputs carefully (since this is a very non-standard application as far as normal Gromacs usage goes) and build the smallest test case you possibly can for each interaction. -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] modify nsteps in an existing tpr file
gmxdump -om writes out a mdp file based on the tpr, but that is not read by grompp. I tried to change or comment out mdp options that are not recognized by grompp. It is attached here. The simulation soon crashes with LINCS errors after 25 steps, while the original tpr runs properly. I'm not sure what's missing here. On Tue, Sep 17, 2013 at 6:12 PM, Mark Abraham mark.j.abra...@gmail.comwrote: No. Theoretically useful, but not implemented. Mark On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. Is it possible to dump the parameters in the tpr file to a mdp file? On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham mark.j.abra...@gmail.com wrote: mdrun -nsteps in 4.6 overrides the number of steps in the .tpr Mark On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I'm new to Gromacs. So apologies if this question is too simple. I downloaded top/tpr files from the supplementary material of a published paper. The nsteps set in the tpr file is 100ns. I wish to do a small test run. Is there any way I can modify that? I've tried to create a mdp file that best matches the parameters found through gmxdump, but it gives me a lot of LINCS error. I can upload the mdp file and gmxdump file if you are kind to help. Thanks in advance. Best regards, -- Guanglei Cui -- 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 -- Guanglei Cui -- 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 -- Guanglei Cui -- 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] segfault on Gromacs 4.6.3 (cuda)
Thanks very much, Szilárd. Our IT just found out we purchased the latest Intel compiler, but apparently was never installed. Now, I can check if this happens with the new compiler. I may or may not follow up with a bug report if I can't reproduce the behavior. Regards, On Sun, Sep 15, 2013 at 1:39 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: Hi, On Tue, Sep 10, 2013 at 2:03 AM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Hi Szilard, Thanks again for getting back. You may remember the previous thread I started on regression test failure with icc 11.x compiled binary. Falling As it was not referenced, I did not recall your previous mail at the time of writing my above reply. back to SSE2 is my solution, and binaries compiled this way are able to pass all regression tests, including the one with GPU switched on. However, it is not clear to me if the GPU part is specifically tested in the regression. In the regression test runs mdrun uses automated selection of CPU or GPU - the same way as it would happen if you were doing a standalone run. Your question reminds me that we should probably extend this behaviour so that when a GPU is present not only the GPU Verlet scheme kernels will be used in the testing. Therefore, my I advise is that regression tests on machines with a GPU and a GPU-enable builds should, for now, be done in two passes: - tests using GPU Verlet kernels: make check; - tests using CPU Verlet kernels: CUDA_VISIBLE_DEVICES= make check (or use GMX_DISABLE_GPU_DETECTION in case of detection issues) As I was trying to explain in the original email, the binary works fine on a node with proper graphics driver, but crashes on a node where the graphics driver is older than the CUDA SDK used in compilation. I think updating the driver may potentially enable the GPU part. Pure CPU I understood, that's what my comment regarding the less than graceful handling of some GPU detection cases. We'll improve this behaviour in one of the upcoming versions. calculation with the same binary seems not working. It is not clear to me if this is caused by the compiler. It's not really simple to update the gcc to 4.7 or greater since we use CentOS 5.x in the company. Even CentOS 6.x uses gcc 4.4.x as default. I've just tested the code with -nb cpu. It still crashes. The binary Have you tried setting the aforementioned environment variable, GMX_DISABLE_GPU_DETECTION? compiled without GPU works as expected and passed all regression tests. For now, I can keep separate binaries for GPU and CPU applications before I can get gcc 4.7 or greater installed. Have you built the correctly functioning mdrun without GPU support on the same machine with the same compiler and libraries as your problematic GPU-enabled builds? While performance-wise it is far from the best choice, AFAIK gcc 4.4 should work OK - at least in our automated tests it does. Hence, the fact that you are using gcc 4.4 should not result in a crash when switching to a CPU-only run. I would appreciate if you could open an issue on redmine.gromacs.org, describe the behaviour you are seeing, and provide as many of the following information as possible: - log files produced with the crashing binary; - result of running with GMX_DISABLE_GPU_DETECTION; - a backtrace of the crash (build with CMAKE_BUILD_TYPE=RelWithDebInfo, run in gdb, type bt after the crash occurs and provide the output) and/or - run with mdrun -debug 1 and provide the mdrun.debug output. With the above information we should be able to judge what is causing the problem. Cheers, -- Szilárd Best regards, Guanglei On Mon, Sep 9, 2013 at 4:35 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: HI, First of all, icc 11 is not well tested and there have been reports about it compiling broken code. This could explain the crash, but you'd need to do a bit more testing to confirm. Regading the GPU detection error, if you use a driver which is incompatible with the CUDA runtime (at least as high API version, see the mdrun log header's last two lines) and at the moment, some of such cases are not detected particularly gracefully. A few things to try: - use gcc, 4.7 is as fast or faster than any icc; - run with the -nb cpu option; does it still crash? - run with GPU detection completely disabled* - run the regressiontests; try using CPUs only* *You can set the GMX_DISABLE_GPU_DETECTION environment variable to completely disable the GPU detection. Cheers, -- Szilárd On Mon, Sep 9, 2013 at 9:52 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I recently compiled Gromacs 4.6.3 with CUDA (Intel compiler 11.x, SSE2, and CUDA SDK 5.0.35). I was doing a test run with simply 'mdrun -deffnm eq2_npt_verlet' (letting mdrun figure out what to use). I received the error telling me my graphics driver was older than
[gmx-users] Re: periodic molecule
Bonds are harmonic. I can test it by restraining them? For purpose of testing I can even make the topology bond to be 2.06, as in the input file. My system shouldn't be any different from a mice sheet, for instance. Both have Metal - O bonds that continue through the sheet. What do you mean by the original geometry - obv it shall be slightly changing through the MD. Shall I be on Gromacs Dev sub-forum to get more insights on how the periodic_molecule works? Or may be could I ask person who implemented that part? I would really like to get it working in Gromacs, rather than having to change the engine. Thank you, V -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011288.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: periodic molecule
On 9/18/13 9:57 AM, Valentina wrote: Bonds are harmonic. I can test it by restraining them? For purpose of testing I can even make the topology bond to be 2.06, as in the input file. Constraints would probably fail, given the relatively large change in geometry. You can try, but I'd suspect it will crash. My system shouldn't be any different from a mice sheet, for instance. Both have Metal - O bonds that continue through the sheet. What do you mean by the original geometry - obv it shall be slightly changing through the MD. Original geometry = what you are providing for coordinates. Shall I be on Gromacs Dev sub-forum to get more insights on how the periodic_molecule works? Or may be could I ask person who implemented that part? I would really like to get it working in Gromacs, rather than having to change the engine. If you want to talk about code, the development list is the right place for the discussion, but I know that periodic_molecules should work, given previous (solved) issues on the list and the fact that I made a simple CNT work at one point. Have a look through the code and if there are any obvious (or non-obvious!) issues, please report back via gmx-developers. -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] Re: periodic molecule
On restraining bonds: The atom moves across the basic unit, i.e. it is not recognising that it should bond via periodic_molecule Error: The charge group starting at atom 2833 moved than the distance allowed by the domain decomposition (1.615483) in direction X In any case (restraining or not all-bonds) when I am doing grompp, I get a warning - WARNING 1 [file LDH21/em.mdp]: The sum of the two largest charge group radii (1.062153) is larger than rlist (1.00) I decided to take it as a healthy one, as according to http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb this is because of Molecules are broken across periodic boundaries, which is not a problem in a periodic system. In this case, the sum of the two largest charge groups will correspond to a value of twice the box vector along which the molecule is broken. -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011290.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] modify nsteps in an existing tpr file
That -om mechanism has been broken for about a decade, unfortunately. You will need to include the file, or post a link a file, not attach it, if you want users of this list to see it. gmxcheck to compare your new and old .tpr files is useful to see what you might need in the new .mdp file to reproduce the first one. Note that grompp -c yourold.tpr is the best way to get the same starting coordinates. Mark On Wed, Sep 18, 2013 at 3:48 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: gmxdump -om writes out a mdp file based on the tpr, but that is not read by grompp. I tried to change or comment out mdp options that are not recognized by grompp. It is attached here. The simulation soon crashes with LINCS errors after 25 steps, while the original tpr runs properly. I'm not sure what's missing here. On Tue, Sep 17, 2013 at 6:12 PM, Mark Abraham mark.j.abra...@gmail.comwrote: No. Theoretically useful, but not implemented. Mark On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. Is it possible to dump the parameters in the tpr file to a mdp file? On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham mark.j.abra...@gmail.com wrote: mdrun -nsteps in 4.6 overrides the number of steps in the .tpr Mark On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I'm new to Gromacs. So apologies if this question is too simple. I downloaded top/tpr files from the supplementary material of a published paper. The nsteps set in the tpr file is 100ns. I wish to do a small test run. Is there any way I can modify that? I've tried to create a mdp file that best matches the parameters found through gmxdump, but it gives me a lot of LINCS error. I can upload the mdp file and gmxdump file if you are kind to help. Thanks in advance. Best regards, -- Guanglei Cui -- 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 -- Guanglei Cui -- 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 -- Guanglei Cui -- 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: periodic molecule
Update https://docs.google.com/file/d/0B6Qm4snFANimcmxYVnBOSkNCd2s/edit?usp=sharing Seems I had to declare the atoms in .rtp with + and - when they are across periodic boundary. The new movie is showing that atoms do move, but not across the box. Yes, I would have to play a little ore with parameters for the system (ongoing work), but the major problem with PBC is sorted. I am giving below my new (working) molecule.rtp file, that is different from the earlier one - may be once this it may be helpful for someone;) Thanks! [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 0 0 [ B21 ] ;# ldh21 [ atoms ] ; atomname atomtype charge chargegroup o1 oc18 -0.875 3 h1 hoy0.350 3 o2 oc17 -0.875 3 h2 hoy0.350 3 o3 oc20 -0.875 3 h3 hoy0.350 3 o4 oc21 -0.875 1 h4 hoy0.350 1 o5 oc16 -0.875 1 h5 hoy0.350 1 o6 oc19 -0.875 1 h6 hoy0.350 1 mg1 mg1.400 al1 ac3 1.351 mg2 mg1.400 o7 oc16 -0.875 2 h7 hoy0.350 2 o8 oc19 -0.875 2 h8 hoy0.350 2 o9 oc18 -0.875 1 h9 hoy0.350 1 o10 oc17 -0.875 1 h10 hoy0.350 1 o11 oc20 -0.875 1 h11 hoy0.350 1 o12 oc21 -0.875 2 h12 hoy0.350 2 mg3 mg1.400 mg4 mg1.400 al2 ac3 1.352 o13 oc20 -0.875 2 h13 hoy0.350 2 o14 oc21 -0.875 3 h14 hoy0.350 3 o15 oc16 -0.875 3 h15 hoy0.350 3 o16 oc19 -0.875 3 h16 hoy0.350 3 o17 oc18 -0.875 2 h17 hoy0.350 2 o18 oc17 -0.875 2 h18 hoy0.350 2 al3 ac3 1.353 mg5 mg1.400 mg6 mg1.400 [ bonds ] ; atom1 atom2 parametersindex o1 h1 b_oc-h o2 h2 b_oc-h o3 h3 b_oc-h o4 h4 b_oc-h o5 h5 b_oc-h o6 h6 b_oc-h o7 h7 b_oc-h o8 h8 b_oc-h o9 h9 b_oc-h o10 h10 b_oc-h o11 h11 b_oc-h o12 h12 b_oc-h o13 h13 b_oc-h o14 h14 b_oc-h o15 h15 b_oc-h o16 h16 b_oc-h o17 h17 b_oc-h o18 h18 b_oc-h al3 +o1 b_ac-oc al3 +o2 b_ac-oc al3 +o3 b_ac-oc o4 al1 b_ac-oc o5 al1 b_ac-oc o6 al1 b_ac-oc al2 -o7 b_ac-oc al2 -o8 b_ac-oc o9 al1 b_ac-oc o10 al1 b_ac-oc o11 al1 b_ac-oc o12 al2 b_ac-oc al2 -o13 b_ac-oc o14 al3 b_ac-oc o15 al3 b_ac-oc o16 al3 b_ac-oc o17 al2 b_ac-oc o18 al2 b_ac-oc [ angles ] ; aiajak gromos type al3 o14 h14 a_ac-oc-h al3 o15 h15 a_ac-oc-h al3 +o1 +h1 a_ac-oc-h al3 o16 h16 a_ac-oc-h al3 +o2 +h2 a_ac-oc-h al3 +o3 +h3 a_ac-oc-h al1 o4 h4 a_ac-oc-h al1 o5 h5 a_ac-oc-h al1 o9 h9 a_ac-oc-h al1 o6 h6 a_ac-oc-h al1 o10 h10 a_ac-oc-h al1 o11 h11 a_ac-oc-h al2 o12 h12 a_ac-oc-h al2 -o7 -h7 a_ac-oc-h al2 o17 h17 a_ac-oc-h al2 -o8 -h8 a_ac-oc-h al2 o18 h18 a_ac-oc-h al2 -o13 -h13 a_ac-oc-h o5 al1 o10 a_oc-ac-oc_1 -o7 al2 o18 a_oc-ac-oc_1 o15 al3 +o2 a_oc-ac-oc_1 o9 al1 o6 a_oc-ac-oc_1 o17 al2 -o8 a_oc-ac-oc_1 +o1 al3 o16 a_oc-ac-oc_1 o11 al1 o4 a_oc-ac-oc_1 -o13al2 o12 a_oc-ac-oc_1 +o3 al3 o14 a_oc-ac-oc_1 o5 al1 o9 a_oc-ac-oc_2 -o7 al2 o17 a_oc-ac-oc_2 o15 al3 +o1 a_oc-ac-oc_2 o5 al1 o4 a_oc-ac-oc_2 -o7 al2 o12 a_oc-ac-oc_2 o15 al3 o14 a_oc-ac-oc_2 o10 al1 o6 a_oc-ac-oc_2 o18 al2 -o8 a_oc-ac-oc_2 +o2 al3 o16 a_oc-ac-oc_2 o10 al1 o11 a_oc-ac-oc_2 o18 al2 -o13a_oc-ac-oc_2 +o2 al3 +o3 a_oc-ac-oc_2 o9 al1 o4 a_oc-ac-oc_2 o17 al2 o12 a_oc-ac-oc_2 +o1 al3 o14 a_oc-ac-oc_2 o6 al1 o11 a_oc-ac-oc_2 -o8 al2 -o13a_oc-ac-oc_2 o16 al3 +o3 a_oc-ac-oc_2 o5 al1 o6 a_oc-ac-oc_3 -o7 al2 -o8 a_oc-ac-oc_3 o15 al3 o16 a_oc-ac-oc_3 o5 al1 o11 a_oc-ac-oc_3 -o7 al2 -o13a_oc-ac-oc_3 o15 al3 +o3 a_oc-ac-oc_3 o10 al1 o9 a_oc-ac-oc_3 o18 al2 o17 a_oc-ac-oc_3 +o2 al3 +o1 a_oc-ac-oc_3 o10 al1 o4 a_oc-ac-oc_3 o18 al2 o12 a_oc-ac-oc_3 +o2 al3 o14 a_oc-ac-oc_3 o9 al1 o11 a_oc-ac-oc_3 o17 al2 -o13a_oc-ac-oc_3 +o1 al3 +o3 a_oc-ac-oc_3 o6 al1 o4 a_oc-ac-oc_3 -o8 al2 o12 a_oc-ac-oc_3 o16 al3 o14 a_oc-ac-oc_3 -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011291.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
Re: [gmx-users] BGQ compilation with verlet kernels: #include file kernel_impl.h not found.
Thanks for the follow up. The take-home lesson is that building for BlueGene/Q is unlike building for the usual homogenous x86 cluster. You still need an MPI and non-MPI build, but the latter should be targeted at the front end (Linux on PowerPC, usually), unless/until GROMACS tools acquire MPI functionality useful on a BlueGene/Q scale. Mark On Wed, Sep 18, 2013 at 2:07 AM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Indeed, it works just fine when I compile with mpi. I never thought to check that. My usual procedure is to compile the whole package without mpi and then to compile mdrun with mpi. Thanks for the help Mark. Here is the compilation script that worked for me. module purge module load vacpp/12.1 xlf/14.1 mpich2/xl module load cmake/2.8.8 module load fftw/3.3.2 export FFTW_LOCATION=/scinet/bgq/Libraries/fftw-3.3.2 cmake ../source/ \ -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \ -DCMAKE_PREFIX_PATH=$FFTW_LOCATION \ -DCMAKE_INSTALL_PREFIX=$(pwd) \ -DGMX_X11=OFF \ -DGMX_MPI=ON \ -DGMX_PREFER_STATIC_LIBS=ON make -j 16 make install -- 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] modify nsteps in an existing tpr file
Thanks. gmxcheck is quite helpful. Here is part of the output. It turns out the difference is mainly in the force field parameters, which indicates the top file provided may not be the one used to produce the tpr file. Perhaps it is best to contact the authors, unless the difference is due to certain changes between gmx 4.0.x and gmx 4.6.3. inputrec-nsteps (5000 - 5000) inputrec-nstcalclr (5 - 0) inputrec-nstdhdl (1 - 50) inputrec-fepvals-init_fep_state ( 0.0e+00 - -1.0e+00) inputrec-fepvals-lambda_neighbors[1] (0 - 1) inputrec-fepvals-sc_power (0 - 1) inputrec-dihre_fc (1.00e+03 - 0.00e+00) inputrec-grpopts.ngtc (4 - 1) inputrec-grpopts.ngener (4 - 1) inputrec-grpopts.nrdf[ 0] (8.610900e+04 - 2.136210e+05) idef-iparam[12]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[12]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[54]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[54]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[82]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[82]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[96]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[96]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[124]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[124]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[152]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[152]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[166]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[166]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[168]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[168]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[171]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[171]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[173]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[173]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[174]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[174]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[176]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[176]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[178]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[178]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[179]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[179]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[180]1: c6= 6.22385694e-03, c12= 5.03394313e-06 idef-iparam[180]2: c6= 2.05496373e-24, c12= 0.e+00 idef-iparam[181]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[181]2: c6= 3.50750256e-08, c12= 5.46337281e-13 idef-iparam[194]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[194]2: c6= 3.50750256e-08, c12= 5.46337281e-13 ... On Wed, Sep 18, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.comwrote: That -om mechanism has been broken for about a decade, unfortunately. You will need to include the file, or post a link a file, not attach it, if you want users of this list to see it. gmxcheck to compare your new and old .tpr files is useful to see what you might need in the new .mdp file to reproduce the first one. Note that grompp -c yourold.tpr is the best way to get the same starting coordinates. Mark On Wed, Sep 18, 2013 at 3:48 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: gmxdump -om writes out a mdp file based on the tpr, but that is not read by grompp. I tried to change or comment out mdp options that are not recognized by grompp. It is attached here. The simulation soon crashes with LINCS errors after 25 steps, while the original tpr runs properly. I'm not sure what's missing here. On Tue, Sep 17, 2013 at 6:12 PM, Mark Abraham mark.j.abra...@gmail.com wrote: No. Theoretically useful, but not implemented. Mark On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. Is it possible to dump the parameters in the tpr file to a mdp file? On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham mark.j.abra...@gmail.com wrote: mdrun -nsteps in 4.6 overrides the number of steps in the .tpr Mark On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I'm new to Gromacs. So apologies if this question is too simple. I downloaded top/tpr files from the supplementary material of a published paper. The nsteps set in the tpr file is 100ns. I wish to do a small test run. Is there any way I can modify that? I've tried to create a mdp file that best matches the parameters found through gmxdump, but it gives me a lot of LINCS error. I can upload the mdp file and gmxdump file if you are kind to help. Thanks in advance. Best regards, -- Guanglei Cui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Re: [gmx-users] modify nsteps in an existing tpr file
There are technical differences between versions about how the VDW parameters are computed. You should not expect .tpr equivalence between minor version changes such as 4.0 and 4.6. You need to compile a 4.0.x grompp to see if your setup is equivalent, but having done so you should be able to use the same inputs to 4.6 grompp and get a correct simulation with 4.6 mdrun. Mark On Wed, Sep 18, 2013 at 1:55 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. gmxcheck is quite helpful. Here is part of the output. It turns out the difference is mainly in the force field parameters, which indicates the top file provided may not be the one used to produce the tpr file. Perhaps it is best to contact the authors, unless the difference is due to certain changes between gmx 4.0.x and gmx 4.6.3. inputrec-nsteps (5000 - 5000) inputrec-nstcalclr (5 - 0) inputrec-nstdhdl (1 - 50) inputrec-fepvals-init_fep_state ( 0.0e+00 - -1.0e+00) inputrec-fepvals-lambda_neighbors[1] (0 - 1) inputrec-fepvals-sc_power (0 - 1) inputrec-dihre_fc (1.00e+03 - 0.00e+00) inputrec-grpopts.ngtc (4 - 1) inputrec-grpopts.ngener (4 - 1) inputrec-grpopts.nrdf[ 0] (8.610900e+04 - 2.136210e+05) idef-iparam[12]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[12]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[54]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[54]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[82]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[82]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[96]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[96]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[124]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[124]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[152]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[152]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[166]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[166]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[168]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[168]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[171]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[171]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[173]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[173]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[174]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[174]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[176]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[176]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[178]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[178]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[179]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[179]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[180]1: c6= 6.22385694e-03, c12= 5.03394313e-06 idef-iparam[180]2: c6= 2.05496373e-24, c12= 0.e+00 idef-iparam[181]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[181]2: c6= 3.50750256e-08, c12= 5.46337281e-13 idef-iparam[194]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[194]2: c6= 3.50750256e-08, c12= 5.46337281e-13 ... On Wed, Sep 18, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.comwrote: That -om mechanism has been broken for about a decade, unfortunately. You will need to include the file, or post a link a file, not attach it, if you want users of this list to see it. gmxcheck to compare your new and old .tpr files is useful to see what you might need in the new .mdp file to reproduce the first one. Note that grompp -c yourold.tpr is the best way to get the same starting coordinates. Mark On Wed, Sep 18, 2013 at 3:48 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: gmxdump -om writes out a mdp file based on the tpr, but that is not read by grompp. I tried to change or comment out mdp options that are not recognized by grompp. It is attached here. The simulation soon crashes with LINCS errors after 25 steps, while the original tpr runs properly. I'm not sure what's missing here. On Tue, Sep 17, 2013 at 6:12 PM, Mark Abraham mark.j.abra...@gmail.com wrote: No. Theoretically useful, but not implemented. Mark On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. Is it possible to dump the parameters in the tpr file to a mdp file? On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham mark.j.abra...@gmail.com wrote: mdrun -nsteps in 4.6 overrides the number of steps in the .tpr Mark On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I'm new to Gromacs. So apologies if this question is too simple. I downloaded top/tpr files from the supplementary material of a published paper. The nsteps set in the tpr file is 100ns. I wish to
Re: [gmx-users] modify nsteps in an existing tpr file
hmm, does that mean the gmx force field file format or specifications are not backward compatible? On Wed, Sep 18, 2013 at 4:08 PM, Mark Abraham mark.j.abra...@gmail.comwrote: There are technical differences between versions about how the VDW parameters are computed. You should not expect .tpr equivalence between minor version changes such as 4.0 and 4.6. You need to compile a 4.0.x grompp to see if your setup is equivalent, but having done so you should be able to use the same inputs to 4.6 grompp and get a correct simulation with 4.6 mdrun. Mark On Wed, Sep 18, 2013 at 1:55 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. gmxcheck is quite helpful. Here is part of the output. It turns out the difference is mainly in the force field parameters, which indicates the top file provided may not be the one used to produce the tpr file. Perhaps it is best to contact the authors, unless the difference is due to certain changes between gmx 4.0.x and gmx 4.6.3. inputrec-nsteps (5000 - 5000) inputrec-nstcalclr (5 - 0) inputrec-nstdhdl (1 - 50) inputrec-fepvals-init_fep_state ( 0.0e+00 - -1.0e+00) inputrec-fepvals-lambda_neighbors[1] (0 - 1) inputrec-fepvals-sc_power (0 - 1) inputrec-dihre_fc (1.00e+03 - 0.00e+00) inputrec-grpopts.ngtc (4 - 1) inputrec-grpopts.ngener (4 - 1) inputrec-grpopts.nrdf[ 0] (8.610900e+04 - 2.136210e+05) idef-iparam[12]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[12]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[54]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[54]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[82]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[82]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[96]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[96]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[124]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[124]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[152]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[152]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[166]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[166]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[168]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[168]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[171]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[171]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[173]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[173]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[174]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[174]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[176]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[176]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[178]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[178]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[179]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[179]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[180]1: c6= 6.22385694e-03, c12= 5.03394313e-06 idef-iparam[180]2: c6= 2.05496373e-24, c12= 0.e+00 idef-iparam[181]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[181]2: c6= 3.50750256e-08, c12= 5.46337281e-13 idef-iparam[194]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[194]2: c6= 3.50750256e-08, c12= 5.46337281e-13 ... On Wed, Sep 18, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.com wrote: That -om mechanism has been broken for about a decade, unfortunately. You will need to include the file, or post a link a file, not attach it, if you want users of this list to see it. gmxcheck to compare your new and old .tpr files is useful to see what you might need in the new .mdp file to reproduce the first one. Note that grompp -c yourold.tpr is the best way to get the same starting coordinates. Mark On Wed, Sep 18, 2013 at 3:48 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: gmxdump -om writes out a mdp file based on the tpr, but that is not read by grompp. I tried to change or comment out mdp options that are not recognized by grompp. It is attached here. The simulation soon crashes with LINCS errors after 25 steps, while the original tpr runs properly. I'm not sure what's missing here. On Tue, Sep 17, 2013 at 6:12 PM, Mark Abraham mark.j.abra...@gmail.com wrote: No. Theoretically useful, but not implemented. Mark On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. Is it possible to dump the parameters in the tpr file to a mdp file? On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham mark.j.abra...@gmail.com wrote: mdrun -nsteps in 4.6 overrides the number of steps in the .tpr Mark On Tue, Sep 17, 2013 at
Re: [gmx-users] modify nsteps in an existing tpr file
Implementation and description of a model physics are two different things. You could compute KE of a particle with 0.5 * m * v^2, but if the mass is used nowhere else, why wouldn't you pre-multiply the mass by 0.5? Mark On Wed, Sep 18, 2013 at 4:31 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: hmm, does that mean the gmx force field file format or specifications are not backward compatible? On Wed, Sep 18, 2013 at 4:08 PM, Mark Abraham mark.j.abra...@gmail.comwrote: There are technical differences between versions about how the VDW parameters are computed. You should not expect .tpr equivalence between minor version changes such as 4.0 and 4.6. You need to compile a 4.0.x grompp to see if your setup is equivalent, but having done so you should be able to use the same inputs to 4.6 grompp and get a correct simulation with 4.6 mdrun. Mark On Wed, Sep 18, 2013 at 1:55 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. gmxcheck is quite helpful. Here is part of the output. It turns out the difference is mainly in the force field parameters, which indicates the top file provided may not be the one used to produce the tpr file. Perhaps it is best to contact the authors, unless the difference is due to certain changes between gmx 4.0.x and gmx 4.6.3. inputrec-nsteps (5000 - 5000) inputrec-nstcalclr (5 - 0) inputrec-nstdhdl (1 - 50) inputrec-fepvals-init_fep_state ( 0.0e+00 - -1.0e+00) inputrec-fepvals-lambda_neighbors[1] (0 - 1) inputrec-fepvals-sc_power (0 - 1) inputrec-dihre_fc (1.00e+03 - 0.00e+00) inputrec-grpopts.ngtc (4 - 1) inputrec-grpopts.ngener (4 - 1) inputrec-grpopts.nrdf[ 0] (8.610900e+04 - 2.136210e+05) idef-iparam[12]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[12]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[54]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[54]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[82]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[82]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[96]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[96]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[124]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[124]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[152]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[152]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[166]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[166]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[168]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[168]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[171]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[171]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[173]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[173]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[174]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[174]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[176]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[176]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[178]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[178]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[179]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[179]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[180]1: c6= 6.22385694e-03, c12= 5.03394313e-06 idef-iparam[180]2: c6= 2.05496373e-24, c12= 0.e+00 idef-iparam[181]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[181]2: c6= 3.50750256e-08, c12= 5.46337281e-13 idef-iparam[194]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[194]2: c6= 3.50750256e-08, c12= 5.46337281e-13 ... On Wed, Sep 18, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.com wrote: That -om mechanism has been broken for about a decade, unfortunately. You will need to include the file, or post a link a file, not attach it, if you want users of this list to see it. gmxcheck to compare your new and old .tpr files is useful to see what you might need in the new .mdp file to reproduce the first one. Note that grompp -c yourold.tpr is the best way to get the same starting coordinates. Mark On Wed, Sep 18, 2013 at 3:48 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: gmxdump -om writes out a mdp file based on the tpr, but that is not read by grompp. I tried to change or comment out mdp options that are not recognized by grompp. It is attached here. The simulation soon crashes with LINCS errors after 25 steps, while the original tpr runs properly. I'm not sure what's missing here. On Tue, Sep 17, 2013 at 6:12 PM, Mark Abraham mark.j.abra...@gmail.com wrote: No. Theoretically useful, but not implemented. Mark On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui amber.mail.arch...@gmail.com
Re: [gmx-users] modify nsteps in an existing tpr file
It is only a simple question, not a criticism of any kind. I'm sure there may be perfect reasons to choose one implementation over another. To someone who is not familiar with the history of gmx development, it is something to be aware of. That's all. On Wed, Sep 18, 2013 at 4:56 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Implementation and description of a model physics are two different things. You could compute KE of a particle with 0.5 * m * v^2, but if the mass is used nowhere else, why wouldn't you pre-multiply the mass by 0.5? Mark On Wed, Sep 18, 2013 at 4:31 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: hmm, does that mean the gmx force field file format or specifications are not backward compatible? On Wed, Sep 18, 2013 at 4:08 PM, Mark Abraham mark.j.abra...@gmail.com wrote: There are technical differences between versions about how the VDW parameters are computed. You should not expect .tpr equivalence between minor version changes such as 4.0 and 4.6. You need to compile a 4.0.x grompp to see if your setup is equivalent, but having done so you should be able to use the same inputs to 4.6 grompp and get a correct simulation with 4.6 mdrun. Mark On Wed, Sep 18, 2013 at 1:55 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. gmxcheck is quite helpful. Here is part of the output. It turns out the difference is mainly in the force field parameters, which indicates the top file provided may not be the one used to produce the tpr file. Perhaps it is best to contact the authors, unless the difference is due to certain changes between gmx 4.0.x and gmx 4.6.3. inputrec-nsteps (5000 - 5000) inputrec-nstcalclr (5 - 0) inputrec-nstdhdl (1 - 50) inputrec-fepvals-init_fep_state ( 0.0e+00 - -1.0e+00) inputrec-fepvals-lambda_neighbors[1] (0 - 1) inputrec-fepvals-sc_power (0 - 1) inputrec-dihre_fc (1.00e+03 - 0.00e+00) inputrec-grpopts.ngtc (4 - 1) inputrec-grpopts.ngener (4 - 1) inputrec-grpopts.nrdf[ 0] (8.610900e+04 - 2.136210e+05) idef-iparam[12]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[12]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[54]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[54]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[82]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[82]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[96]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[96]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[124]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[124]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[152]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[152]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[166]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[166]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[168]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[168]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[171]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[171]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[173]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[173]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[174]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[174]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[176]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[176]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[178]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[178]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[179]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[179]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[180]1: c6= 6.22385694e-03, c12= 5.03394313e-06 idef-iparam[180]2: c6= 2.05496373e-24, c12= 0.e+00 idef-iparam[181]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[181]2: c6= 3.50750256e-08, c12= 5.46337281e-13 idef-iparam[194]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[194]2: c6= 3.50750256e-08, c12= 5.46337281e-13 ... On Wed, Sep 18, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.com wrote: That -om mechanism has been broken for about a decade, unfortunately. You will need to include the file, or post a link a file, not attach it, if you want users of this list to see it. gmxcheck to compare your new and old .tpr files is useful to see what you might need in the new .mdp file to reproduce the first one. Note that grompp -c yourold.tpr is the best way to get the same starting coordinates. Mark On Wed, Sep 18, 2013 at 3:48 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: gmxdump -om writes out a mdp file based on the tpr, but that is not read by grompp. I tried to change or comment out mdp options
[gmx-users] Selecting certain types of atoms from trajectory file with C++ code
Dear users, Recently I have been trying to use xdrfile libray to read trajectory .trr file in my own C++ code. Now I can just read the coordinates of all atoms at each time frame. But I don't know how to select certain types of atoms from the trajectory file. Although the graomcs tool make_ndx can do this, but i need to do it with C++ codes for the purpose of further analysis. Does someone have any experience about this? Your reply would be greatly appreciated. Thanks, Zhikun -- 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: gmx-users Digest, Vol 113, Issue 81
Re: [gmx-users] BGQ compilation with verlet kernels: #include filekernel_impl.h not found. Side note: On a Blue Gene/Q machine this particular version of Gromacs is 2.5x times faster than the regular one. I really hope thw BGQ accelerated kernels will go into the main branch soon. Best, Jernej On Wed, Sep 18, 2013 at 11:40 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to 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 You can reach the person managing the list at 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. Re: periodic molecule (Valentina) 2. Re: Re: periodic molecule (Justin Lemkul) 3. Re: periodic molecule (Valentina) 4. Re: modify nsteps in an existing tpr file (Mark Abraham) 5. Re: periodic molecule (Valentina) 6. Re: BGQ compilation with verlet kernels: #include file kernel_impl.h not found. (Mark Abraham) -- Message: 1 Date: Wed, 18 Sep 2013 06:57:11 -0700 (PDT) From: Valentina valentina.erast...@durham.ac.uk Subject: [gmx-users] Re: periodic molecule To: gmx-users@gromacs.org Message-ID: 1379512631663-5011288.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Bonds are harmonic. I can test it by restraining them? For purpose of testing I can even make the topology bond to be 2.06, as in the input file. My system shouldn't be any different from a mice sheet, for instance. Both have Metal - O bonds that continue through the sheet. What do you mean by the original geometry - obv it shall be slightly changing through the MD. Shall I be on Gromacs Dev sub-forum to get more insights on how the periodic_molecule works? Or may be could I ask person who implemented that part? I would really like to get it working in Gromacs, rather than having to change the engine. Thank you, V -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011288.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Message: 2 Date: Wed, 18 Sep 2013 10:01:39 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re: periodic molecule To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 5239b243.4050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 9/18/13 9:57 AM, Valentina wrote: Bonds are harmonic. I can test it by restraining them? For purpose of testing I can even make the topology bond to be 2.06, as in the input file. Constraints would probably fail, given the relatively large change in geometry. You can try, but I'd suspect it will crash. My system shouldn't be any different from a mice sheet, for instance. Both have Metal - O bonds that continue through the sheet. What do you mean by the original geometry - obv it shall be slightly changing through the MD. Original geometry = what you are providing for coordinates. Shall I be on Gromacs Dev sub-forum to get more insights on how the periodic_molecule works? Or may be could I ask person who implemented that part? I would really like to get it working in Gromacs, rather than having to change the engine. If you want to talk about code, the development list is the right place for the discussion, but I know that periodic_molecules should work, given previous (solved) issues on the list and the fact that I made a simple CNT work at one point. Have a look through the code and if there are any obvious (or non-obvious!) issues, please report back via gmx-developers. -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 == -- Message: 3 Date: Wed, 18 Sep 2013 07:10:39 -0700 (PDT) From: Valentina valentina.erast...@durham.ac.uk Subject: [gmx-users] Re: periodic molecule To: gmx-users@gromacs.org Message-ID: 1379513439478-5011290.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii On restraining bonds: The atom moves across the basic unit, i.e. it is not recognising that it should bond via periodic_molecule Error: The charge group starting at atom 2833 moved than the distance allowed by the domain decomposition (1.615483) in direction X In any case (restraining or not all-bonds) when I am
