[gmx-users] memory excess error of Tip4p/Ice model
Dear gromacs users I have performed MD simulation using Tip4p/ice model, which is copied from [http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_topology_file_for_the_TIP4P/Ice_model] The MD actually works and the output structure looks fine. However, after 11ns run, the run was suddenly stopped and I got the following error message. In case of Tip4p, in which .top file contains #include ffoplsaa.itp #include tip4p.itp the MD run works well and never stop, although I used the same .mdp and .gro file. The difference of two MD runs is just .top file, so I suspect .top file for tip4p/ice has something wrong. Could you please give me advise to fix it ? Regards Error tput: No value for $TERM and no -T specified = PBS: job killed: mem 33310024kb exceeded limit 32505856kb === .top file [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 1.0 1.0 [atomtypes] ;name mass charge ptypesigmaepsilon IW 0 0.000 D 0.0 0.0 OWT4 15.99940 0.000 A 0.31668 0.88211 HW 1.00800 0.000 A 0.0E+00 0.0E+00 [moleculetype] ; name nrexcl SOL 1 [atoms] ; nr type resnr residu atom cgnr charge 1 OWT4 1 water OW 1 0 15.994 2 HW 1 water HW1 1 0.58971.008 3 HW 1 water HW2 1 0.58971.008 4 IW 1 water MW 1-1.17940.0 [constraints] ;i j funct doh dhh 1 2 1 0.09572 1 3 1 0.09572 2 3 1 0.15139 [exclusions] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 [dummies3] ; Dummy fromfunct a b 4 1 2 3 1 0.13458 0.13458 [system] water TIP4P/Ice [molecules] SOL 433 = Kenji -- 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] Diffusion beyond periodic boundary
Dear Tsjerk Thank you very much, -pbc nojump works well. Is it possible to select the specific molecule for -pbc nojump ? For example, the coordinates of water molecules are rewind and the LJ particles are NOT rewind ? Regards Kenji - Original Message - From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: 2013-02-09 17:24:23 Subject: Re: [gmx-users] Diffusion beyond periodic boundary Hi Kenji, You can remove the jumps/rewinds using 'trjconv -pbc nojump'. Cheers, Tsjerk On Sat, Feb 9, 2013 at 4:45 AM, Kenji Mochizuki kmo...@ims.ac.jp wrote: Dear All I have performed MD run with periodic boundary condition, which system is consist of water and LJ particles. I would like to know the time dependence of the dislocated distance (diffusion) from the starting time (t=0). Firstly, I made pdb file of the trajectory, then calculated the distance from pdb file. However, when the particle goes beyond periodic boundary, the x-y-z coordination is rewind into the box size. So, the dislocated distance is wrong. Could you please tell me how to calculate the dislocated distance accurately ? Best regards Kenji -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists National Institutes of Natural Sciences Institute for Molecular Science Kenji Mochizuki e-mail: kmo...@ims.ac.jp phone: 0564-55-7394 -- 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] Diffusion beyond periodic boundary
Dear Tsjerk Thank you for reply. I will make PDB using -pbc nojump and rewind only the selected molecules by own program. Thank you Kenji - Original Message - From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: 2013-02-09 19:17:12 Subject: Re: [gmx-users] Diffusion beyond periodic boundary Hi Kenji, That's not possible. But why would you need that? It's not very hard to make the changes required in gmx_trjconv.c Cheers, Tsjerk On Sat, Feb 9, 2013 at 9:37 AM, Kenji Mochizuki kmo...@ims.ac.jp wrote: Dear Tsjerk Thank you very much, -pbc nojump works well. Is it possible to select the specific molecule for -pbc nojump ? For example, the coordinates of water molecules are rewind and the LJ particles are NOT rewind ? Regards Kenji - Original Message - From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: 2013-02-09 17:24:23 Subject: Re: [gmx-users] Diffusion beyond periodic boundary Hi Kenji, You can remove the jumps/rewinds using 'trjconv -pbc nojump'. Cheers, Tsjerk On Sat, Feb 9, 2013 at 4:45 AM, Kenji Mochizuki kmo...@ims.ac.jp wrote: Dear All I have performed MD run with periodic boundary condition, which system is consist of water and LJ particles. I would like to know the time dependence of the dislocated distance (diffusion) from the starting time (t=0). Firstly, I made pdb file of the trajectory, then calculated the distance from pdb file. However, when the particle goes beyond periodic boundary, the x-y-z coordination is rewind into the box size. So, the dislocated distance is wrong. Could you please tell me how to calculate the dislocated distance accurately ? Best regards Kenji -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists National Institutes of Natural Sciences Institute for Molecular Science Kenji Mochizuki e-mail: kmo...@ims.ac.jp phone: 0564-55-7394 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists National Institutes of Natural Sciences Institute for Molecular Science Kenji Mochizuki e-mail: kmo...@ims.ac.jp phone: 0564-55-7394 -- 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] Diffusion beyond periodic boundary
Dear All I have performed MD run with periodic boundary condition, which system is consist of water and LJ particles. I would like to know the time dependence of the dislocated distance (diffusion) from the starting time (t=0). Firstly, I made pdb file of the trajectory, then calculated the distance from pdb file. However, when the particle goes beyond periodic boundary, the x-y-z coordination is rewind into the box size. So, the dislocated distance is wrong. Could you please tell me how to calculate the dislocated distance accurately ? Best regards Kenji -- 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] making .top file of new LJ in Water
Dear gmx users I would like to start MD simulation for GAS Hydrate, consisting of TIP4P and LJ representing N2. I have made .top file by hand as following. When I use grompp_d for making .tpr file, I got the following error. However, LJ name in .gro file is same as in .top file, which is NX I am not sure what is wrong. Could you please give me some advise ? Regards === error === WARNING 1 [file GAS_Hydrate.top, line 25]: 4353 non-matching atom names atom names from GAS_Hydrate.top will be used atom names from N1088-N2.gro will be ignored === .top file #include ffoplsaa.itp ;Nitrogen Molecule- [ atomtypes ] NX NX 0. 0. A 3.69800e-01 0.787014e+00 [ moleculetype ] LJN 3 [ atoms ] 1 NX 1LJN NX 10.0 28.00 ;--- TIP4P -- #include tip4p.itp [ system ] GAS Hydrate [ molecules ] LJN 1 SOL 1088 ==- Kenji Mochizuki -- 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] making .top file of new LJ in Water
Dear EB Thank you very much. Now, it works and looks OK to me. Regards Kenji - Original Message - From: Emanuel Birru emanuel.bi...@monash.edu To: 'Discussion list for GROMACS users' gmx-users@gromacs.org Date: 2013-01-28 14:04:37 Subject: RE: [gmx-users] making .top file of new LJ in Water Hi Kenji, I guess if you change/swap the order of molecules in top file it will work. The order of molecules in your gro file should match up with your top file. If you give us more info it would be good :) I am just guessing :( [ molecules ] SOL 1088 LJN 1 Swap them like this Cheers, EB -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Kenji Mochizuki Sent: Monday, 28 January 2013 3:46 PM To: gmx-users@gromacs.org Subject: [gmx-users] making .top file of new LJ in Water Dear gmx users I would like to start MD simulation for GAS Hydrate, consisting of TIP4P and LJ representing N2. I have made .top file by hand as following. When I use grompp_d for making .tpr file, I got the following error. However, LJ name in .gro file is same as in .top file, which is NX I am not sure what is wrong. Could you please give me some advise ? Regards === error === WARNING 1 [file GAS_Hydrate.top, line 25]: 4353 non-matching atom names atom names from GAS_Hydrate.top will be used atom names from N1088-N2.gro will be ignored === .top file #include ffoplsaa.itp ;Nitrogen Molecule- [ atomtypes ] NX NX 0. 0. A 3.69800e-01 0.787014e+00 [ moleculetype ] LJN 3 [ atoms ] 1 NX 1LJN NX 10.0 28.00 ;--- TIP4P -- #include tip4p.itp [ system ] GAS Hydrate [ molecules ] LJN 1 SOL 1088 ==- Kenji Mochizuki -- 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 National Institutes of Natural Sciences Institute for Molecular Science Kenji Mochizuki e-mail: kmo...@ims.ac.jp phone: 0564-55-7394 -- 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] How to merge Self-made ammonia .top with tip4p
Dear GMX users Could you tell me how to make the topology file for ammonia in tip4p water? I made topology file for ammonia by hand, as shown at end. MD dose work when system has only ammonia molecules. For ammonia in water, I had though it needed to add just two line at the top of .top file. #include ffoplsaa.itp #include tip4p.itp However, I got Invalid order for directive defaults in using grompp_d. Should I add this new atoms information into ffnonbonded.itp directly ?? ;[ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon FNFN 0. 0. A 3.39000e-01 1.414192e+00 FHFH 0. 0. A 0.0e+00 0.0e+00 [ moleculetype ] ; Namenrexcl AM 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 FN 1AM N 1 -1.03500 14.00 2 FH 1AM H1 30.34500 1.00 3 FH 1AM H2 40.34500 1.00 4 FH 1AM H3 50.34500 1.00 [ bonds ] ; aiaj funct r k 1 2 1 1.0124e-01 5.0242e+05 1 3 1 1.0124e-01 5.0242e+05 1 4 1 1.0124e-01 5.0242e+05 [ pairs ] ; aiaj funct [ angles ] ; aiajak funct theta cth 2 1 3 1 1.0670e+02 6.2802e+02 2 1 4 1 1.0670e+02 6.2802e+02 3 1 4 1 1.0670e+02 6.2802e+02 [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 [ system ] ammonia [ molecules ] AM 11 K.Mochi -- 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] How to merge Self-made ammonia .top with tip4p
Dear Justin Thank you for reply. I added #include ffoplsaa.itp into top and #include tip4p.itpafter [exclusions], as you told. Then, I could make tpr file and MD looks working. Thank you very much. Kenji - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Date: 2012-12-06 22:56:19 Subject: Re: [gmx-users] How to merge Self-made ammonia .top with tip4p On 12/6/12 6:09 AM, Kenji Mochizuki wrote: Dear GMX users Could you tell me how to make the topology file for ammonia in tip4p water? I made topology file for ammonia by hand, as shown at end. MD dose work when system has only ammonia molecules. For ammonia in water, I had though it needed to add just two line at the top of .top file. #include ffoplsaa.itp #include tip4p.itp However, I got Invalid order for directive defaults in using grompp_d. Should I add this new atoms information into ffnonbonded.itp directly ?? That should not be necessary. If your [defaults] directive is properly commented out (as shown), you shouldn't get this error. The order of inclusion is important. You have to define all force field-level directives (e.g., [defaults], [atomtypes], etc) before you can define any [moleculetypes], so you can't #include tip4p.itp until after the ammonia parameters, since you're introducing new [atomtypes] for that molecule. The easiest solution is simply to move that #include statement right after the end of the ammonia [moleculetype] definition (see below). ;[ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon FNFN 0. 0. A 3.39000e-01 1.414192e+00 FHFH 0. 0. A 0.0e+00 0.0e+00 [ moleculetype ] ; Namenrexcl AM 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 FN 1AM N 1 -1.03500 14.00 2 FH 1AM H1 30.34500 1.00 3 FH 1AM H2 40.34500 1.00 4 FH 1AM H3 50.34500 1.00 [ bonds ] ; aiaj funct r k 1 2 1 1.0124e-01 5.0242e+05 1 3 1 1.0124e-01 5.0242e+05 1 4 1 1.0124e-01 5.0242e+05 [ pairs ] ; aiaj funct [ angles ] ; aiajak funct theta cth 2 1 3 1 1.0670e+02 6.2802e+02 2 1 4 1 1.0670e+02 6.2802e+02 3 1 4 1 1.0670e+02 6.2802e+02 [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 Add #include tip4p.itp here. -Justin [ system ] ammonia [ molecules ] AM 11 K.Mochi -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists National Institutes of Natural Sciences Institute for Molecular Science Kenji Mochizuki e-mail: kmo...@ims.ac.jp phone: 0564-55-7394 -- 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
