[gmx-users] drawing the plots
hello dear Gromacs users i have Gromacs4.5.3 installed on suse11.1.but when i run commands like g_gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvgi can't see any plot drawn. although the command is run with no error. by the way i have the package package xmgrace-5.1.21-27.91.x86_64 already installed. thanks! sajad -- 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] Adding water to protein to start the simulation process
Hey :) I see that I never stated to run the production run... But at that point in the tutorial there have been several equilibration runs already, so it should be trivial to figure it out. Yet I'll add a small paragraph at the end of the production run section. Thanks for the interest in the tutorial. I hope it's good for you. Cheers, Tsjerk On Apr 15, 2011 10:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: Monisha Hajra wrote: Hi Justin, I am trying to follow the protocol only. More than the Gromacs own website, I find http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production link is more useful. Clearly. This is one of many tutorials linked from the site I posted before. However, I am stuck at one step which is mentioned : http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html I am not able to understand how to create traj.trr, traj.xtc and ener.edr file. Remaining all is self explained in the previous link. These files are output by mdrun, i.e. actually running a simulation. -Justin Really appreciate any help. Regards Monisha On Fri, Apr 15, 2011 at 8:06 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu ... jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==... mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt... mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Schol... -- 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] Fatal error: number of coordinates in coordinate file does not match topology
Dear Justin, I have 6 EDO and 1 TRS ligans. I created coordinate and .itp files for eachEDO molecule using prodrg web server. Then I created 6 .itp files as EDO1.itp, EDO2.itp.EDO6.itp. I changed residue numbers. But I have Fatal Error moleculetype EDO is redefined. Am I on the wrong track?:-( *EDO1.itp:* [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO O1 1 -0.163 15.9994 2H 1 EDO HAA 10.074 1.0080 3 CH2 1 EDO C1 10.089 14.0270 4 CH2 1 EDO C2 20.089 14.0270 5OA 1 EDO O2 2 -0.163 15.9994 6H 1 EDO HAB 20.074 1.0080 *EDO2.itp:* [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 2 EDO O1 1 -0.163 15.9994 2H2 EDO HAA 10.074 1.0080 3 CH2 2 EDO C1 10.089 14.0270 4 CH2 2 EDO C2 20.089 14.0270 5OA 2 EDO O2 2 -0.163 15.9994 6H2 EDO HAB 20.074 1.0080 *topol.top*: ... #include EDO1.itp #include EDO2.itp #include EDO3.itp #include EDO4.itp #include EDO5.itp #include EDO6.itp #include TRS.itp ... [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 EDO 6 TRS 1 SOL 185 SOL 143 SOL 33713 *conf.gro:* MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5384 2GLN N1 1.458 -1.158 0.739 2GLN H12 1.520 -1.083 0.763 485HOHHW1 5333 0.221 -3.864 -2.291 485HOHHW2 5334 0.303 -3.946 -2.407 1EDO O1 1 0.625 -3.071 -0.171 1EDO HAA 2 0.698 -3.048 -0.107 1EDO C1 3 0.596 -3.211 -0.163 1EDO C2 4 0.486 -3.247 -0.261 1EDO O2 5 0.365 -3.179 -0.224 1EDO HAB 6 0.292 -3.203 -0.288 2EDO O1 1 2.023 -4.300 0.220 2EDO HAA 2 2.046 -4.296 0.317 2EDO C1 3 2.138 -4.342 0.146 2EDO C2 4 2.096 -4.347 -0.001 2EDO O2 5 2.196 -4.412 -0.079 2EDO HAB 6 2.167 -4.415 -0.174 3EDO O1 1 2.502 -3.407 -2.265 3EDO HAA 2 2.529 -3.365 -2.178 3EDO C1 3 2.466 -3.303 -2.359 3EDO C2 4 2.424 -3.364 -2.492 3EDO O2 5 2.294 -3.423 -2.477 3EDO HAB 6 2.265 -3.464 -2.564 4EDO O1 1 1.021 -5.733 -2.007 4EDO HAA 2 0.952 -5.780 -2.061 4EDO C1 3 0.995 -5.753 -1.868 4EDO C2 4 1.102 -5.679 -1.787 4EDO O2 5 1.091 -5.540 -1.816 4EDO HAB 6 1.160 -5.489 -1.764 5EDO O1 1 1.988 -3.117 -3.247 5EDO HAA 2 1.915 -3.177 -3.217 5EDO C1 3 2.100 -3.194 -3.291 5EDO C2 4 2.212 -3.102 -3.337 5EDO O2 5 2.247 -3.012 -3.231 5EDO HAB 6 2.321 -2.952 -3.261 6EDO O1 1 0.987 -4.579 -0.020 6EDO HAA 2 0.969 -4.622 -0.109 6EDO C1 3 1.118 -4.521 -0.021 6EDO C2 4 1.145 -4.456 0.114 6EDO O2 5 1.054 -4.506 0.212 6EDO HAB 6 1.073 -4.463 0.300 1TRS O1 1 1.825 -3.900 0.047 1TRS HAA 2 1.853 -3.860 -0.040 1TRS C1 3 1.712 -3.977 0.028 1TRS C4 1.659 -4.044 0.150 1TRS C3 5 1.576 -3.946 0.226 1TRS O3 6 1.634 -3.824 0.256 1TRS HAC 7 1.569 -3.768 0.307 1TRS N8 1.582 -4.159 0.113 1TRS HAE 9 1.547 -4.204 0.195 1TRS HAF 10 1.505 -4.131 0.056 1TRS HAD 11 1.639 -4.223 0.062 1TRS C2 12 1.776 -4.085 0.233 1TRS O2 13 1.887 -4.122 0.160 1TRS HAB 14 1.961 -4.148 0.222 8.13100 7.04165 13.54850 0.0 0.0 -4.06550 0.0 0.0 0.0 14 Nisan 2011 21:09 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı: ahmet yıldırım wrote: Dear Justin, Thanks for your valuable helps. How should I rearranged the conf.gro file for 6 EDO ligand? is the following conf.gro mistake? Well, it's certainly not working, is it? You only have one EDO molecule shown here. Is this the only one? If it is, then you need to build the system to reflect what you actually want to do. No one on this list can tell you that. You have to build a starting configuration that fits the goals of your study. -Justin _*conf.gro:*_ MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5354 2GLN N1 1.458 -1.158 0.739 2GLN H12 1.520 -1.083 0.763 ... 485HOHHW1 5333 0.221 -3.864 -2.291 485HOHHW2 5334 0.303
Re: [gmx-users] drawing the plots
xmgrace gyrate.xvg On Sat, Apr 16, 2011 at 2:09 PM, Sajad Ahrari sajadahr...@yahoo.com wrote: hello dear Gromacs users i have Gromacs4.5.3 installed on suse11.1.but when i run commands like g_gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg i can't see any plot drawn. although the command is run with no error. by the way i have the package package xmgrace-5.1.21-27.91.x86_64 already installed. thanks! sajad gmx-users@gromacs.org -- 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] error in running jobs in parallel !!!
Dear Justin thanks for your previous explanations. We are running job with gromacs in parallel. after having the outpus of the first run, when submitting the jobs for the next 10ns we encounter with this error. can you help me to fix that. Pleas let me know the possible reasons to see this kind of error. Thanks Best wishes D. Aghaie tarting mdrun '3840 water (TIP4P-2005) molecules' 500 steps, 1.0 ps. NOTE: Turning on dynamic load balancing [HPC-0-12.local:26592] *** An error occurred in MPI_Waitall [HPC-0-12.local:26592] *** on communicator MPI_COMM_WORLD [HPC-0-12.local:26592] *** MPI_ERR_TRUNCATE: message truncated [HPC-0-12.local:26592] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) -- mpirun has exited due to process rank 2 with PID 26592 on node HPC-0-12 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). --- On Sat, 4/16/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] the ligand have more than one molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, April 16, 2011, 3:38 AM ahmet yıldırım wrote: Dear users, Is there anyone has a tutorial of the ligand have more than one molecules? Perhaps you can describe in more detail what it is you hope to accomplish. The procedure for dealing with multiple ligands is, in principle, no different from a single ligand. There are not tutorials available for every variation of a procedure. -Justin For example: *_topol.top:_* [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 *ligandname * 3 Thanks in advance -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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] suitable forcefield
dear users I going to simulate a Kinase protein with MG_ATP as co-factor. do you have any idea witch force field of Gromacs4.5.3 would be most suitable? -- 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 in running jobs in parallel !!!
On 16/04/2011 7:06 PM, delara aghaie wrote: Dear Justin thanks for your previous explanations. We are running job with gromacs in parallel. after having the outpus of the first run, when submitting the jobs for the next 10ns we encounter with this error. can you help me to fix that. Pleas let me know the possible reasons to see this kind of error. Anything could cause that - including some problem with the hardware - and we can see no diagnostic information. Look at the .log file also. Try to run the .tpr in serial. Mark Thanks Best wishes D. Aghaie *tarting mdrun '3840 water (TIP4P-2005) molecules' 500 steps, 1.0 ps.* *NOTE: Turning on dynamic load balancing* *[HPC-0-12.local:26592] *** An error occurred in MPI_Waitall [HPC-0-12.local:26592] *** on communicator MPI_COMM_WORLD [HPC-0-12.local:26592] *** MPI_ERR_TRUNCATE: message truncated [HPC-0-12.local:26592] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) -- mpirun has exited due to process rank 2 with PID 26592 on node HPC-0-12 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). *--- On *Sat, 4/16/11, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] the ligand have more than one molecules To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, April 16, 2011, 3:38 AM ahmet yıldırım wrote: Dear users, Is there anyone has a tutorial of the ligand have more than one molecules? Perhaps you can describe in more detail what it is you hope to accomplish. The procedure for dealing with multiple ligands is, in principle, no different from a single ligand. There are not tutorials available for every variation of a procedure. -Justin For example: *_topol.top:_* [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 *ligandname * 3 Thanks in advance -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-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 http://us.mc1301.mail.yahoo.com/mc/compose?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] Fatal error: number of coordinates in coordinate file does not match topology
On 16/04/2011 6:05 PM, ahmet yıldırım wrote: Dear Justin, I have 6 EDO and 1 TRS ligans. I created coordinate and .itp files for each EDO moleculeusing prodrg web server. Then I created 6 .itp files as EDO1.itp, EDO2.itp.EDO6.itp. Why? The fragment [molecules] EDO 6 is what specifies six identical EDO molecules. Your earlier problem was in matching the contents of your [molecules] section with your coordinate file. They have to contain the same molecules in the same order. I changed residue numbers. But I have Fatal Error moleculetype EDO is redefined. Am I on the wrong track?:-( So don't re-define moleculetype EDO. Mark _*EDO1.itp:*_ [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO O1 1 -0.163 15.9994 2H 1 EDO HAA 10.074 1.0080 3 CH2 1 EDO C1 10.089 14.0270 4 CH2 1 EDO C2 20.089 14.0270 5OA 1 EDO O2 2 -0.163 15.9994 6H 1 EDO HAB 20.074 1.0080 *_EDO2.itp:_* [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 2 EDO O1 1 -0.163 15.9994 2H2 EDO HAA 10.074 1.0080 3 CH2 2 EDO C1 10.089 14.0270 4 CH2 2 EDO C2 20.089 14.0270 5OA 2 EDO O2 2 -0.163 15.9994 6H2 EDO HAB 20.074 1.0080 _*topol.top*_: ... #include EDO1.itp #include EDO2.itp #include EDO3.itp #include EDO4.itp #include EDO5.itp #include EDO6.itp #include TRS.itp ... [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 EDO 6 TRS 1 SOL 185 SOL 143 SOL 33713 _*conf.gro:*_ MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5384 2GLN N1 1.458 -1.158 0.739 2GLN H12 1.520 -1.083 0.763 485HOHHW1 5333 0.221 -3.864 -2.291 485HOHHW2 5334 0.303 -3.946 -2.407 1EDO O1 1 0.625 -3.071 -0.171 1EDO HAA 2 0.698 -3.048 -0.107 1EDO C1 3 0.596 -3.211 -0.163 1EDO C2 4 0.486 -3.247 -0.261 1EDO O2 5 0.365 -3.179 -0.224 1EDO HAB 6 0.292 -3.203 -0.288 2EDO O1 1 2.023 -4.300 0.220 2EDO HAA 2 2.046 -4.296 0.317 2EDO C1 3 2.138 -4.342 0.146 2EDO C2 4 2.096 -4.347 -0.001 2EDO O2 5 2.196 -4.412 -0.079 2EDO HAB 6 2.167 -4.415 -0.174 3EDO O1 1 2.502 -3.407 -2.265 3EDO HAA 2 2.529 -3.365 -2.178 3EDO C1 3 2.466 -3.303 -2.359 3EDO C2 4 2.424 -3.364 -2.492 3EDO O2 5 2.294 -3.423 -2.477 3EDO HAB 6 2.265 -3.464 -2.564 4EDO O1 1 1.021 -5.733 -2.007 4EDO HAA 2 0.952 -5.780 -2.061 4EDO C1 3 0.995 -5.753 -1.868 4EDO C2 4 1.102 -5.679 -1.787 4EDO O2 5 1.091 -5.540 -1.816 4EDO HAB 6 1.160 -5.489 -1.764 5EDO O1 1 1.988 -3.117 -3.247 5EDO HAA 2 1.915 -3.177 -3.217 5EDO C1 3 2.100 -3.194 -3.291 5EDO C2 4 2.212 -3.102 -3.337 5EDO O2 5 2.247 -3.012 -3.231 5EDO HAB 6 2.321 -2.952 -3.261 6EDO O1 1 0.987 -4.579 -0.020 6EDO HAA 2 0.969 -4.622 -0.109 6EDO C1 3 1.118 -4.521 -0.021 6EDO C2 4 1.145 -4.456 0.114 6EDO O2 5 1.054 -4.506 0.212 6EDO HAB 6 1.073 -4.463 0.300 1TRS O1 1 1.825 -3.900 0.047 1TRS HAA 2 1.853 -3.860 -0.040 1TRS C1 3 1.712 -3.977 0.028 1TRS C4 1.659 -4.044 0.150 1TRS C3 5 1.576 -3.946 0.226 1TRS O3 6 1.634 -3.824 0.256 1TRS HAC 7 1.569 -3.768 0.307 1TRS N8 1.582 -4.159 0.113 1TRS HAE 9 1.547 -4.204 0.195 1TRS HAF 10 1.505 -4.131 0.056 1TRS HAD 11 1.639 -4.223 0.062 1TRS C2 12 1.776 -4.085 0.233 1TRS O2 13 1.887 -4.122 0.160 1TRS HAB 14 1.961 -4.148 0.222 8.13100 7.04165 13.54850 0.0 0.0 -4.06550 0.0 0.0 0.0 14 Nisan 2011 21:09 tarihinde Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu yazdı: ahmet yıldırım wrote: Dear Justin, Thanks for your valuable helps. How should I rearranged the conf.gro file for 6 EDO ligand? is the following conf.gro mistake? Well, it's certainly not working, is it? You only have one EDO molecule shown here. Is this the only one? If it is, then you
Re: [gmx-users] suitable forcefield
On 16/04/2011 7:11 PM, Sajad Ahrari wrote: dear users I going to simulate a Kinase protein with MG_ATP as co-factor. do you have any idea witch force field of Gromacs4.5.3 would be most suitable? Sounds like a job for a literature search, to me :-) Mark -- 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 in running jobs in parallel !!!
Dear Mark What do you mean by running .tpr in serial? Thanks in advance D.aghaie --- On Sat, 4/16/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] error in running jobs in parallel !!! To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, April 16, 2011, 1:42 PM On 16/04/2011 7:06 PM, delara aghaie wrote: Dear Justin thanks for your previous explanations. We are running job with gromacs in parallel. after having the outpus of the first run, when submitting the jobs for the next 10ns we encounter with this error. can you help me to fix that. Pleas let me know the possible reasons to see this kind of error. Anything could cause that - including some problem with the hardware - and we can see no diagnostic information. Look at the .log file also. Try to run the .tpr in serial. Mark -- 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 in running jobs in parallel !!!
On 16/04/2011 7:21 PM, delara aghaie wrote: Dear Mark What do you mean by running .tpr in serial? The opposite of parallel. Mark Thanks in advance D.aghaie --- On *Sat, 4/16/11, Mark Abraham /mark.abra...@anu.edu.au/* wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] error in running jobs in parallel !!! To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, April 16, 2011, 1:42 PM On 16/04/2011 7:06 PM, delara aghaie wrote: Dear Justin thanks for your previous explanations. We are running job with gromacs in parallel. after having the outpus of the first run, when submitting the jobs for the next 10ns we encounter with this error. can you help me to fix that. Pleas let me know the possible reasons to see this kind of error. Anything could cause that - including some problem with the hardware - and we can see no diagnostic information. Look at the .log file also. Try to run the .tpr in serial. Mark -- 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] ions problem
Dear users, I am using gromacs 4.5.3. Initially I removed ligands from pdb file. Then I started to simulation .I met such a problem ( last error) after I added ions. What could be the problem? pdb2gmx -f withoutligand_xxx.pdb editconf -f conf.gro -bt cubic -d 1.0 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal Error:* System has non-zero total charge: -1.50e+01 genion -s em.tpr -o solvated.gro -pname NA+ -np 15 -g em.log select: Group 13 (SOL) grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal error:* number of coordinates in coordinate file (solvated.gro, 106473) does not match topology (topol.top, 106518) *topol.top:* .. [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 SOL33723 NA 15 -- Ahmet YILDIRIM -- 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] ions problem
ahmet yıldırım wrote: Dear users, I am using gromacs 4.5.3. Initially I removed ligands from pdb file. Then I started to simulation .I met such a problem ( last error) after I added ions. What could be the problem? pdb2gmx -f withoutligand_xxx.pdb editconf -f conf.gro -bt cubic -d 1.0 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal Error:* System has non-zero total charge: -1.50e+01 genion -s em.tpr -o solvated.gro -pname NA+ -np 15 -g em.log Unless you updated your topology manually after running this command, you haven't accounted for the fact that 15 water molecules are going to be removed. Use the -p flag to have genion make the changes for you. Note that NA+ is incorrect for version 4.5.3 - ion [moleculetype] names have changed since version 4.0.7. select: Group 13 (SOL) grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal error:* number of coordinates in coordinate file (solvated.gro, 106473) does not match topology (topol.top, 106518) The answer to this error is _always_ the same - you haven't accounted properly for some change in the system that has been made to the coordinate file but not the topology. http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology _*topol.top:*_ .. [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 SOL33723 NA 15 Something isn't matching up here. Either your genion command that you showed above is wrong, or this topology snippet has been modified from what genion would produce. Please always copy and paste commands, topology snippets, etc so that we have self-consistent information to help you. -Justin -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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: ions problem
problem solved:) [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 SOL *33708* NA *15* 16 Nisan 2011 21:22 tarihinde ahmet yıldırım ahmedo...@gmail.com yazdı: Dear users, I am using gromacs 4.5.3. Initially I removed ligands from pdb file. Then I started to simulation .I met such a problem ( last error) after I added ions. What could be the problem? pdb2gmx -f withoutligand_xxx.pdb editconf -f conf.gro -bt cubic -d 1.0 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal Error:* System has non-zero total charge: -1.50e+01 genion -s em.tpr -o solvated.gro -pname NA+ -np 15 -g em.log select: Group 13 (SOL) grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal error:* number of coordinates in coordinate file (solvated.gro, 106473) does not match topology (topol.top, 106518) *topol.top:* .. [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 SOL33723 NA 15 -- Ahmet YILDIRIM -- Ahmet YILDIRIM -- 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] ions problem
Dear Justin, Thank you. Problem is solved. I forgot remove ions from SOL numbers. By the way, I used the genion command as genion -s em.tpr -o solvated.gro -pname NA+ -np 15 -g em.log but it correctly worked. Thanks 16 Nisan 2011 21:37 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı: ahmet yıldırım wrote: Dear users, I am using gromacs 4.5.3. Initially I removed ligands from pdb file. Then I started to simulation .I met such a problem ( last error) after I added ions. What could be the problem? pdb2gmx -f withoutligand_xxx.pdb editconf -f conf.gro -bt cubic -d 1.0 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal Error:* System has non-zero total charge: -1.50e+01 genion -s em.tpr -o solvated.gro -pname NA+ -np 15 -g em.log Unless you updated your topology manually after running this command, you haven't accounted for the fact that 15 water molecules are going to be removed. Use the -p flag to have genion make the changes for you. Note that NA+ is incorrect for version 4.5.3 - ion [moleculetype] names have changed since version 4.0.7. select: Group 13 (SOL) grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal error:* number of coordinates in coordinate file (solvated.gro, 106473) does not match topology (topol.top, 106518) The answer to this error is _always_ the same - you haven't accounted properly for some change in the system that has been made to the coordinate file but not the topology. http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology _*topol.top:*_ .. [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 SOL33723 NA 15 Something isn't matching up here. Either your genion command that you showed above is wrong, or this topology snippet has been modified from what genion would produce. Please always copy and paste commands, topology snippets, etc so that we have self-consistent information to help you. -Justin -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- Ahmet YILDIRIM -- 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] ions problem
ahmet yıldırım wrote: Dear Justin, Thank you. Problem is solved. I forgot remove ions from SOL numbers. By the way, I used the genion command as genion -s em.tpr -o solvated.gro -pname NA+ -np 15 -g em.log but it correctly worked. It may have worked but be aware that grompp will later complain about non-matching atom names. In this case, it won't be a significant problem, but you will make your life easier if you follow the naming conventions that are explained in the manual and genion help info: The ion molecule type, residue and atom names in all force fields are the capitalized element names without sign. Ions which can have multiple charge states get the multiplicity added, without sign, for the uncommon states only. -Justin Thanks 16 Nisan 2011 21:37 tarihinde Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu yazdı: ahmet yıldırım wrote: Dear users, I am using gromacs 4.5.3. Initially I removed ligands from pdb file. Then I started to simulation .I met such a problem ( last error) after I added ions. What could be the problem? pdb2gmx -f withoutligand_xxx.pdb editconf -f conf.gro -bt cubic -d 1.0 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal Error:* System has non-zero total charge: -1.50e+01 genion -s em.tpr -o solvated.gro -pname NA+ -np 15 -g em.log Unless you updated your topology manually after running this command, you haven't accounted for the fact that 15 water molecules are going to be removed. Use the -p flag to have genion make the changes for you. Note that NA+ is incorrect for version 4.5.3 - ion [moleculetype] names have changed since version 4.0.7. select: Group 13 (SOL) grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal error:* number of coordinates in coordinate file (solvated.gro, 106473) does not match topology (topol.top, 106518) The answer to this error is _always_ the same - you haven't accounted properly for some change in the system that has been made to the coordinate file but not the topology. http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology _*topol.top:*_ .. [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 185 SOL 143 SOL33723 NA 15 Something isn't matching up here. Either your genion command that you showed above is wrong, or this topology snippet has been modified from what genion would produce. Please always copy and paste commands, topology snippets, etc so that we have self-consistent information to help you. -Justin -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] 1/viscosity from g_energy
Dear gmx-users, I am trying to obtain 1/viscosity values for my system after using the cos_acceleration option in the mdp file. My gromacs version is 4.5.4 released on March 21, 2011. When I try using the g_energy option for my file g_energy -f ener.edr -o outfile.xvg I get the following options End your selection with an empty line or a zero. --- 1 Bond 2 Angle 3 Improper-Dih. 4 LJ-(SR) 5 Disper.-corr. 6 Coulomb-(SR) 7 Potential 8 Kinetic-En. 9 Total-Energy 10 Conserved-En. 11 Temperature 12 Pres.-DC 13 Pressure 14 Box-XX 15 Box-YY 16 Box-ZZ 17 Box-YX 18 Box-ZX 19 Box-ZY 20 Volume 21 Density 22 pV 23 Enthalpy 24 Vir-XX 25 Vir-XY 26 Vir-XZ 27 Vir-YX 28 Vir-YY 29 Vir-YZ 30 Vir-ZX 31 Vir-ZY 32 Vir-ZZ 33 Pres-XX 34 Pres-XY 35 Pres-XZ 36 Pres-YX 37 Pres-YY 38 Pres-YZ 39 Pres-ZX 40 Pres-ZY 41 Pres-ZZ 42 #Surf*SurfTen 43 Mu-X 44 Mu-Y 45 Mu-Z 46 T-System 47 Lamb-System I am not sure which option (1 to 47) gives 1/viscosity. I tried looking through the manual and searching the user list but could not resolve the issue. Please let me know what am I missing here. Thanks, SN -- 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] 1/viscosity from g_energy
shikha nangia wrote: Dear gmx-users, I am trying to obtain 1/viscosity values for my system after using the cos_acceleration option in the mdp file. My gromacs version is 4.5.4 released on March 21, 2011. When I try using the g_energy option for my file g_energy -f ener.edr -o outfile.xvg I get the following options End your selection with an empty line or a zero. --- 1 Bond 2 Angle3 Improper-Dih.4 LJ-(SR) 5 Disper.-corr.6 Coulomb-(SR) 7 Potential8 Kinetic-En. 9 Total-Energy10 Conserved-En. 11 Temperature 12 Pres.-DC 13 Pressure14 Box-XX 15 Box-YY 16 Box-ZZ 17 Box-YX 18 Box-ZX 19 Box-ZY 20 Volume 21 Density 22 pV 23 Enthalpy24 Vir-XX 25 Vir-XY 26 Vir-XZ 27 Vir-YX 28 Vir-YY 29 Vir-YZ 30 Vir-ZX 31 Vir-ZY 32 Vir-ZZ 33 Pres-XX 34 Pres-XY 35 Pres-XZ 36 Pres-YX 37 Pres-YY 38 Pres-YZ 39 Pres-ZX 40 Pres-ZY 41 Pres-ZZ 42 #Surf*SurfTen 43 Mu-X44 Mu-Y 45 Mu-Z46 T-System47 Lamb-System I am not sure which option (1 to 47) gives 1/viscosity. I tried looking through the manual and searching the user list but could not resolve the issue. Please let me know what am I missing here. Use -vis rather than -o. -Justin Thanks, SN -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] 1/viscosity from g_energy
Thanks for your instant reply, Justin.
Dear all,
Please correct me if I am woring herebut...reading through the user-list, I
gathered that -vis option og g_energy oes not give good results and instead
cos_accleration should be used from the following reference.
@Article{Hess2002b,
author = {B. Hess},
title = {Determining the shear viscosity of model liquids from
molecular simulation},
journal ={J. Chem. Phys.},
year = 2002,
volume = 116,
pages = {209-217}
}
I am trying to get the results of viscosity through cos_acceleration that
probably are formatted as below (taken from a user-list).
Energy Average Err.Est. RMSD Tot-Drift
---
1/Viscosity ( s/kg)
Thanks again,
SN
--- On Sat, 4/16/11, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] 1/viscosity from g_energy
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Saturday, April 16, 2011, 3:06 PM
shikha nangia wrote:
Dear gmx-users,
I am trying to obtain 1/viscosity values for my system after using the
cos_acceleration option in the mdp file. My gromacs version is 4.5.4 released
on March 21, 2011.
When I try using the g_energy option for my file
g_energy -f ener.edr -o outfile.xvg
I get the following options
End your selection with an empty line or a zero.
---
1 Bond 2 Angle 3 Improper-Dih. 4 LJ-(SR)
5 Disper.-corr. 6 Coulomb-(SR) 7 Potential 8 Kinetic-En.
9 Total-Energy 10 Conserved-En. 11 Temperature 12 Pres.-DC
13 Pressure 14 Box-XX 15 Box-YY 16 Box-ZZ
17 Box-YX 18 Box-ZX 19 Box-ZY 20 Volume
21 Density 22 pV 23 Enthalpy 24 Vir-XX
25 Vir-XY 26 Vir-XZ 27 Vir-YX 28 Vir-YY
29 Vir-YZ 30 Vir-ZX 31 Vir-ZY 32 Vir-ZZ
33 Pres-XX 34 Pres-XY 35 Pres-XZ 36 Pres-YX
37 Pres-YY 38 Pres-YZ 39
Pres-ZX 40 Pres-ZY 41 Pres-ZZ 42 #Surf*SurfTen 43
Mu-X 44 Mu-Y 45 Mu-Z 46 T-System 47
Lamb-System
I am not sure which option (1 to 47) gives 1/viscosity. I tried looking
through the manual and searching the user list but could not resolve the
issue.
Please let me know what am I missing here.
Use -vis rather than -o.
-Justin
Thanks,
SN
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
-- gmx-users mailing list gmx-users@gromacs.org
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Please search the archive at
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--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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Re: [gmx-users] 1/viscosity from g_energy
shikha nangia wrote:
Thanks for your instant reply, Justin.
Dear all,
Please correct me if I am woring herebut...reading through the
user-list, I gathered that -vis option og g_energy oes not give good
results and instead cos_accleration should be used from the following
reference.
/@Article{Hess2002b,
// author ={B. Hess},
// title = {Determining the shear viscosity of model liquids from
//molecular simulation},
// journal = {J. Chem. Phys.},
// year = 2002,
// volume =116,
// pages = {209-217}
//}
/
I am trying to get the results of viscosity through cos_acceleration
that probably are formatted as below (taken from a user-list).
/ Energy Average Err.Est. RMSD
Tot-Drift
//
---
// 1/Viscosity/ (/ s/kg)
/
If the proper output options are not there, then there may have been a problem
in the .mdp file that prevented the correct energy terms from being written. If
present in the .edr file, it should be shown in the list (sorry, I was thinking
of something else). Please post your .mdp file.
-Justin
Thanks again,
SN
--- On *Sat, 4/16/11, Justin A. Lemkul /jalem...@vt.edu/* wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] 1/viscosity from g_energy
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Saturday, April 16, 2011, 3:06 PM
shikha nangia wrote:
Dear gmx-users,
I am trying to obtain 1/viscosity values for my system after
using the cos_acceleration option in the mdp file. My gromacs
version is 4.5.4 released on March 21, 2011.
When I try using the g_energy option for my file
g_energy -f ener.edr -o outfile.xvg
I get the following options
End your selection with an empty line or a zero.
---
1 Bond 2 Angle3 Improper-Dih.4
LJ-(SR)5 Disper.-corr.6 Coulomb-(SR) 7 Potential
8 Kinetic-En.9 Total-Energy10 Conserved-En. 11
Temperature 12 Pres.-DC 13 Pressure14 Box-XX
15 Box-YY 16 Box-ZZ17 Box-YX 18
Box-ZX 19 Box-ZY 20 Volume21 Density
22 pV 23 Enthalpy24 Vir-XX25
Vir-XY 26 Vir-XZ 27 Vir-YX 28 Vir-YY
29 Vir-YZ 30 Vir-ZX 31 Vir-ZY
32 Vir-ZZ33 Pres-XX 34 Pres-XY 35
Pres-XZ 36 Pres-YX 37 Pres-YY 38 Pres-YZ
39 Pres-ZX 40 Pres-ZY 41 Pres-ZZ 42
#Surf*SurfTen 43 Mu-X44 Mu-Y 45 Mu-Z
46 T-System47 Lamb-System
I am not sure which option (1 to 47) gives 1/viscosity. I tried
looking through the manual and searching the user list but could not
resolve the issue.
Please let me know what am I missing here.
Use -vis rather than -o.
-Justin
Thanks,
SN
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
-- gmx-users mailing listgmx-users@gromacs.org
/mc/compose?to=gmx-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
/mc/compose?to=gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
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[gmx-users] Issues of NEMD + 1/viscosity from g_energy
Thanks again, Justin.
Dear all,
I figured out the problem. Error was in my mdp file options. I did not specify
the acc-groups correctly. I can get 1/viscosity using g_energy.
However, once the acc-groups are specified, now the NEW issue is not being able
to run my job correctly.
I get the following errors:
Step 376, time 7.52 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006964, max 0.163855 (between atoms 861 and 859)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
---
---
Program mdrun, VERSION 4.5.4
Source code file: domdec.c, line: 4124
Fatal error:
A charge group moved too far between two domain decomposition steps
---
I did not have any problems in my equilibrium simulations...this is happening
in NEMD simulations.
Here is my .mdp file
title = Martini
cpp = /usr/bin/cpp
integrator = md
tinit = 0.0
dt = 0.01
nsteps = 500
nstcomm = 1
comm-grps = system
nstxout = 10
nstvout = 10
nstfout = 10
nstlog = 10
nstenergy = 10
nstxtcout = 2500
xtc_precision = 100
xtc-grps =
energygrps = system
nstlist = 1
ns_type = grid
pbc = xyz
rlist = 1.7
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = EnerPres
tcoupl = V-rescale
tc-grps = NGL W
tau_t = 1.0 1.0
ref_t = 300. 300.
Pcoupl = No
Pcoupltype = Isotropic
tau_p = 1.0
compressibility = 1e-5
ref_p = 1.0
gen_vel = Yes
gen_temp = 300
gen_seed = 473529
constraints = None
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 1
lincs_warnangle = 30
; Non-equilibrium MD stuff
acc-grps = NGL W
accelerate = 0.1 0 0 -0.1 0 0
freezegrps =
freezedim =
cos_acceleration = 0.1
deform =
Best,
SN
--- On Sat, 4/16/11, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] 1/viscosity from g_energy
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Saturday, April 16, 2011, 3:27 PM
shikha nangia wrote:
Thanks for your instant reply, Justin.
Dear all,
Please correct me if I am woring herebut...reading through the user-list,
I gathered that -vis option og g_energy oes not give good results and instead
cos_accleration should be used from the following reference.
/@Article{Hess2002b,
// author = {B. Hess},
// title = {Determining the shear viscosity of model liquids from
//molecular simulation},
// journal = {J. Chem. Phys.},
// year = 2002,
// volume = 116,
// pages = {209-217}
//}
/
I am trying to get the results of viscosity through cos_acceleration that
probably are formatted as below (taken from a user-list).
/ Energy Average Err.Est. RMSD
Tot-Drift
//
---
// 1/Viscosity / (/ s/kg)
/
If the proper output options are not there, then there may have been a problem
in the .mdp file that prevented the correct energy terms from being written.
If present in the .edr file, it should be shown in the list (sorry, I was
thinking of something else). Please post your .mdp file.
-Justin
Thanks again,
SN
--- On *Sat, 4/16/11, Justin A. Lemkul /jalem...@vt.edu/* wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] 1/viscosity from g_energy
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Saturday, April 16, 2011, 3:06 PM
shikha nangia wrote:
Dear gmx-users,
I am trying to obtain 1/viscosity values for my system after
using the cos_acceleration option in the mdp file. My gromacs
version is 4.5.4 released on March 21, 2011.
When I try using the g_energy option for my file
g_energy -f ener.edr -o outfile.xvg
I get the following options
End your selection with an empty line or a zero.
---
1 Bond
Re: [gmx-users] Issues of NEMD + 1/viscosity from g_energy
shikha nangia wrote:
Thanks again, Justin.
Dear all,
I figured out the problem. Error was in my mdp file options. I did not
specify the acc-groups correctly. I can get 1/viscosity using g_energy.
However, once the acc-groups are specified, now the NEW issue is not
being able to run my job correctly.
I get the following errors:
Step 376, time 7.52 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006964, max 0.163855 (between atoms 861 and 859)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Whatever you're doing to the system is causing its underlying model physics to
break down. Please see:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
If you want help troubleshooting, please provide:
1. A description of the system
2. Outcomes of energy minimization and equilibration
3. Full .mdp file of the process that is crashing
-Justin
---
---
Program mdrun, VERSION 4.5.4
Source code file: domdec.c, line: 4124
Fatal error:
A charge group moved too far between two domain decomposition steps
---
I did not have any problems in my equilibrium simulations...this is
happening in NEMD simulations.
Here is my .mdp file
title= Martini
cpp = /usr/bin/cpp
integrator = md
tinit= 0.0
dt = 0.01
nsteps = 500
nstcomm = 1
comm-grps = system
nstxout = 10
nstvout = 10
nstfout = 10
nstlog = 10
nstenergy= 10
nstxtcout= 2500
xtc_precision= 100
xtc-grps =
energygrps = system
nstlist = 1
ns_type = grid
pbc = xyz
rlist= 1.7
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r= 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = EnerPres
tcoupl = V-rescale
tc-grps = NGL W
tau_t= 1.0 1.0
ref_t= 300. 300.
Pcoupl = No
Pcoupltype = Isotropic
tau_p= 1.0
compressibility = 1e-5
ref_p= 1.0
gen_vel = Yes
gen_temp = 300
gen_seed = 473529
constraints = None
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 1
lincs_warnangle = 30
; Non-equilibrium MD stuff
acc-grps = NGL W
accelerate = 0.1 0 0 -0.1 0 0
freezegrps =
freezedim=
cos_acceleration = 0.1
deform =
Best,
SN
--- On *Sat, 4/16/11, Justin A. Lemkul /jalem...@vt.edu/* wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] 1/viscosity from g_energy
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Saturday, April 16, 2011, 3:27 PM
shikha nangia wrote:
Thanks for your instant reply, Justin.
Dear all,
Please correct me if I am woring herebut...reading through
the user-list, I gathered that -vis option og g_energy oes not give
good results and instead cos_accleration should be used from the
following reference.
/@Article{Hess2002b,
// author = {B. Hess},
// title = {Determining the shear viscosity of model
liquids from //molecular simulation},
// journal = {J. Chem. Phys.},
// year = 2002,
// volume = 116,
// pages = {209-217}
//}
/
I am trying to get the results of viscosity through
cos_acceleration that probably are formatted as below (taken from a
user-list).
/ Energy Average Err.Est. RMSD
Tot-Drift
//
---
// 1/Viscosity/ (/ s/kg)
/
If the proper output options are not there, then there may have been
a problem in the .mdp file that prevented the correct energy terms
from being written. If present in the .edr file, it should be shown
in the list (sorry, I was thinking of something else). Please post
your .mdp file.
-Justin
Thanks again,
SN
--- On *Sat, 4/16/11, Justin A. Lemkul /jalem...@vt.edu
/mc/compose?to=jalem...@vt.edu/* wrote:
From: Justin A. Lemkul jalem...@vt.edu
/mc/compose?to=jalem...@vt.edu
Subject: Re: [gmx-users]
[gmx-users] Issues with NEMD simulations
Dear all, 1. I am performing MD simulation of a MARTINI coarse grained polymeric chains (named NGL in my mdp file below) in Coarse grained water (named W in mdp file below). 2. My equilibration and MD runs have been running perfectly until now. I have started doing NEMD simulations to get viscosity. The starting structure for NEMD came from an equilibrated system. 3. I am pretty sure that the error is in the mdp file. I am new to NEMD so it will be great if I can get some pointers of solving the issue. Is there a NEMD gromacs tutorial on the web? Here is the full mdp file for the NEMD run: title = Martini cpp = /usr/bin/cpp integrator = md tinit = 0.0 dt = 0.01 nsteps = 500 nstcomm = 1 comm-grps = system nstxout = 10 nstvout = 10 nstfout = 10 nstlog = 10 nstenergy = 10 nstxtcout = 2500 xtc_precision = 100 xtc-grps = energygrps = system nstlist = 1 ns_type = grid pbc = xyz rlist = 1.7 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r = 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = EnerPres tcoupl = V-rescale tc-grps = NGL W tau_t = 1.0 1.0 ref_t = 300. 300. Pcoupl = No Pcoupltype = Isotropic tau_p = 1.0 compressibility = 1e-5 ref_p = 1.0 gen_vel = Yes gen_temp = 300 gen_seed = 473529 constraints = None constraint_algorithm = Lincs unconstrained_start = no lincs_order = 1 lincs_warnangle = 30 ; Non-equilibrium MD stuff acc-grps = NGL W accelerate = 0.1 0 0 -0.1 0 0 freezegrps = freezedim = cos_acceleration = 0.1 deform = Best, SN Dr. Shikha Nangia 201D Chemistry Building Department of Chemistry The Pennsylvania State University University Park, PA 16802 Phone(o): 814-863-0289 Phone(cell): 612-599-9449 -- 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] Issues with NEMD simulations
shikha nangia wrote: Dear all, 1. I am performing MD simulation of a MARTINI coarse grained polymeric chains (named NGL in my mdp file below) in Coarse grained water (named W in mdp file below). 2. My equilibration and MD runs have been running perfectly until now. I have started doing NEMD simulations to get viscosity. The starting structure for NEMD came from an equilibrated system. 3. I am pretty sure that the error is in the mdp file. I am new to NEMD so it will be great if I can get some pointers of solving the issue. Is there a NEMD gromacs tutorial on the web? Not likely. If its not posted on http://www.gromacs.org/Documentation/Tutorials and you can't find it with Google, then it probably doesn't exist, unfortunately. Here is the full mdp file for the NEMD run: title= Martini cpp = /usr/bin/cpp integrator = md tinit= 0.0 dt = 0.01 nsteps = 500 nstcomm = 1 comm-grps = system nstxout = 10 nstvout = 10 nstfout = 10 nstlog = 10 nstenergy= 10 nstxtcout= 2500 xtc_precision= 100 xtc-grps = energygrps = system nstlist = 1 ns_type = grid pbc = xyz rlist= 1.7 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = EnerPres tcoupl = V-rescale tc-grps = NGL W tau_t= 1.0 1.0 ref_t= 300. 300. Pcoupl = No Pcoupltype = Isotropic tau_p= 1.0 compressibility = 1e-5 ref_p= 1.0 gen_vel = Yes Well, you started with an equilibrated system, but then re-generating velocities destroys that. gen_temp = 300 gen_seed = 473529 constraints = None constraint_algorithm = Lincs unconstrained_start = no lincs_order = 1 lincs_warnangle = 30 ; Non-equilibrium MD stuff acc-grps = NGL W accelerate = 0.1 0 0 -0.1 0 0 Are NGL and W mixed? Or are they separate phases? If they're mixed and being pushed in opposite directions, you're just smashing your system together. Even if they're layered, you may be getting nasty collisions at the interface of the two phases. You can investigate the source of the LINCS errors you posted before by following the tips here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System Based on the fact that you're saving every 10 steps, you should be able to get a pretty good look at what's going on, and in conjunction with the atom numbers that the LINCS warnings print, you can pinpoint exactly where everything starts to break down. -Justin freezegrps = freezedim= cos_acceleration = 0.1 deform = Best, SN Dr. Shikha Nangia 201D Chemistry Building Department of Chemistry The Pennsylvania State University University Park, PA 16802 Phone(o): 814-863-0289 Phone(cell): 612-599-9449 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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: 1/viscosity from g_energy
Dear all, I figured out the problem. Error was in my mdp file options. I did not specify the acc-groups correctly. I can get 1/viscosity using g_energy. However, once the acc-groups are specified, now the NEW issue is not being able to run my job correctly. I get the following errors: Step 376, time 7.52 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.006964, max 0.163855 (between atoms 861 and 859) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1. To get viscosity from non-eq. MD, you should specify ONLY cos_acceleration in the MDP and then use g_energy utility. 2, To get viscosity from eq. MD, use g_energy -vis, while saving the energy terms every 10-30 fs. Your problems with lincs are probably connected with a high value for acceleration. The first step is to decrease it. -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- 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] mdrun_mpi in HP_MPI LSF/SLURM setup
On 16/04/2011 12:13 AM, Larcombe, Lee wrote: Hi gmx-users We have an HPC setup running HP_MPI and LSF/SLURM. Gromacs 4.5.3 has been compiled with mpi support The compute nodes on the system contain 2 x dual core Xeons which the system sees as 4 processors An LSF script called gromacs_run.lsf is as shown below #BSUB -N #BSUB -J gromacsTest5 #BSUB -u l.larco...@cranfield.ac.uk #BSUB -n 4 #BSUB -q short #BSUB -o %J.log mpirun -srun mdrun_mpi -v -s xxx.tpr -o xxx.trr Queued with: Bsub gromacs_run.lsf This is intended to run 1 mdrun on a single node using all four cores of the two xeons. The result is that although the job is only submitted to one compute node, 4 mdruns are launched on each of the 4 cores = 16 jobs. These are all the same as if mdrun has not been compiled with mpi support. mdrun_mpi will run one process on each core that the MPI configuration declares is available. Spawning four separate runs of four processes indicates that MPI is not configured to reflect the hardware (since each run thinks it can have four processes), or that the submission script is inappropriate (since four runs get spawned), or both. We can't help there. Trouble-shoot with a trivial MPI test program. If I tell srun to start just one task with mpirun -srun -n1 mdrun_mpi -v -s xxx.tpr –o xxx.trr it starts one job on each core instead of 4: NNODES=1, MYRANK=0, HOSTNAME=comp195 NNODES=1, MYRANK=0, HOSTNAME=comp195 NNODES=1, MYRANK=0, HOSTNAME=comp195 NNODES=1, MYRANK=0, HOSTNAME=comp195 Logs show 4 mdrun_mpi starts, 4 file read ins and I get 4 of all run files in CWD. I am sure that mdrun_mpi is indeed compiled with mpi support - although our sysadmin did that, not me. For example, if I try and execute mdrun_mpi –h I get a message from HP–MPI and have to execute mpirun mdrun_mpi –h to see the help text. Does anyone have any experience of running with this setup - any ideas? Thanks Lee -- 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] Adding Virtual Site to the Molecule
On 15/04/2011 6:05 AM, Sikandar Mashayak wrote: Hi I am thinking of a simulation set up, where I modify a structure/topology of a molecule under consideration, in which, I want to introduce a dummy atom/site which will always be located at center of mass of a molecule and it will only interact with dummy atom of other molecule. COM vsites are already implemented, see manual. To have them interact only with other such dummy atom(s) in other molecules, you will have to use energy groups and energy group exclusions. See manual. Mark -- 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] mdrun_mpi in HP_MPI LSF/SLURM setup
Thanks Mark, HP-MPI is configured correctly on the system - an HP XC 3000 800 cores. It works for all the other users (none gromacs) and no I've tested it, I can launch an mpi job which runs fine on the login node (two quad core xeons) It seems to be an issue with the number of processors passed from the BSUB settings in the LSF script via srun to gromacs. I just wondered whether anyone else had 4.5.3 working in a similar setup? Most of the LSF/SLURM stuff I can google (not much) seems to be pre 4.5 where mdrun_mpi will take the depreciated command line switch to tell it the number of processors Lee == Dr Lee Larcombe - Lecturer in Genetics Computational Biology - London Technology Network Business Fellow - Course Director of MSc Applied Bioinformatics Course website: http://bit.ly/cM6SkT Group Research: http://bit.ly/bfqtyo Bioinformatics Group, Cranfield University Bedfordshire MK43 0AL. T: +44 (0)1234 758320 == On 16/04/2011 22:34, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/04/2011 12:13 AM, Larcombe, Lee wrote: Hi gmx-users We have an HPC setup running HP_MPI and LSF/SLURM. Gromacs 4.5.3 has been compiled with mpi support The compute nodes on the system contain 2 x dual core Xeons which the system sees as 4 processors An LSF script called gromacs_run.lsf is as shown below #BSUB -N #BSUB -J gromacsTest5 #BSUB -u l.larco...@cranfield.ac.uk #BSUB -n 4 #BSUB -q short #BSUB -o %J.log mpirun -srun mdrun_mpi -v -s xxx.tpr -o xxx.trr Queued with: Bsub gromacs_run.lsf This is intended to run 1 mdrun on a single node using all four cores of the two xeons. The result is that although the job is only submitted to one compute node, 4 mdruns are launched on each of the 4 cores = 16 jobs. These are all the same as if mdrun has not been compiled with mpi support. mdrun_mpi will run one process on each core that the MPI configuration declares is available. Spawning four separate runs of four processes indicates that MPI is not configured to reflect the hardware (since each run thinks it can have four processes), or that the submission script is inappropriate (since four runs get spawned), or both. We can't help there. Trouble-shoot with a trivial MPI test program. If I tell srun to start just one task with mpirun -srun -n1 mdrun_mpi -v -s xxx.tpr o xxx.trr it starts one job on each core instead of 4: NNODES=1, MYRANK=0, HOSTNAME=comp195 NNODES=1, MYRANK=0, HOSTNAME=comp195 NNODES=1, MYRANK=0, HOSTNAME=comp195 NNODES=1, MYRANK=0, HOSTNAME=comp195 Logs show 4 mdrun_mpi starts, 4 file read ins and I get 4 of all run files in CWD. I am sure that mdrun_mpi is indeed compiled with mpi support - although our sysadmin did that, not me. For example, if I try and execute mdrun_mpi h I get a message from HPMPI and have to execute mpirun mdrun_mpi h to see the help text. Does anyone have any experience of running with this setup - any ideas? Thanks Lee -- 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] genbox output taking forever to complete
Dear All, I am trying to add a single strand dna, and single walled carbon nanotube in a box using the genbox command. After typing following command: genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o cntdna.gro, I get: Reading solute configuration Containing 168 atoms in 1 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration Giving Russians Opium May Alter Current Situation solvent configuration contains 648 atoms in 216 residues and then it takes forever to produce output. I tried to generate an output with just one molecule in solvent (spc216.gro), and I ran into same problem. I suspect something is wrong with my solvent input (file attached). I copied this file from gromacs/tutor/water folder, though it looks reasonable when I view I view the corresponding .pdb file in rasmol (I created .gro file from .pdb file using editconf -f spc216.pdb -o spc216.gro). Could anyone please guide me about possible issues, and how to resolve them? Thank You, Majid spc216.gro Description: Binary data -- 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] genbox output taking forever to complete
majid hasan wrote: Dear All, I am trying to add a single strand dna, and single walled carbon nanotube in a box using the genbox command. After typing following command: genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o cntdna.gro, I get: Reading solute configuration Containing 168 atoms in 1 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration Giving Russians Opium May Alter Current Situation solvent configuration contains 648 atoms in 216 residues and then it takes forever to produce output. I tried to generate an output with just one molecule in solvent (spc216.gro), and I ran into same problem. I suspect something is wrong with my solvent input (file attached). I copied this file from gromacs/tutor/water folder, though it looks reasonable when I view I view the corresponding .pdb file in rasmol (I created .gro file from .pdb file using editconf -f spc216.pdb -o spc216.gro). Could anyone please guide me about possible issues, and how to resolve them? You're asking genbox to do far too many things at once. Divide your procedure into steps: 1. Set a box size using editconf for either the CNT or DNA. 2. Place DNA into box with CNT using genbox -ci -nmol 1 (or vice versa: CNT into DNA box, whichever order you want) 3. Solvate -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] genbox output taking forever to complete
Justin A. Lemkul wrote: majid hasan wrote: Dear All, I am trying to add a single strand dna, and single walled carbon nanotube in a box using the genbox command. After typing following command: genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o cntdna.gro, I get: Reading solute configuration Containing 168 atoms in 1 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration Giving Russians Opium May Alter Current Situation solvent configuration contains 648 atoms in 216 residues and then it takes forever to produce output. I tried to generate an output with just one molecule in solvent (spc216.gro), and I ran into same problem. I suspect something is wrong with my solvent input (file attached). I copied this file from gromacs/tutor/water folder, though it looks reasonable when I view I view the corresponding .pdb file in rasmol (I created .gro file from .pdb file using editconf -f spc216.pdb -o spc216.gro). Could anyone please guide me about possible issues, and how to resolve them? You're asking genbox to do far too many things at once. Divide your procedure into steps: 1. Set a box size using editconf for either the CNT or DNA. I should say a sensible box size - a 2x2x2 box barely accommodates the smallest DNA fragment, and then certainly does not leave any room at all to accommodate the minimum image convention. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] genbox output taking forever to complete
Okay, thanks Justin!. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sat, April 16, 2011 6:19:39 PM Subject: Re: [gmx-users] genbox output taking forever to complete Justin A. Lemkul wrote: majid hasan wrote: Dear All, I am trying to add a single strand dna, and single walled carbon nanotube in a box using the genbox command. After typing following command: genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o cntdna.gro, I get: Reading solute configuration Containing 168 atoms in 1 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration Giving Russians Opium May Alter Current Situation solvent configuration contains 648 atoms in 216 residues and then it takes forever to produce output. I tried to generate an output with just one molecule in solvent (spc216.gro), and I ran into same problem. I suspect something is wrong with my solvent input (file attached). I copied this file from gromacs/tutor/water folder, though it looks reasonable when I view I view the corresponding .pdb file in rasmol (I created .gro file from .pdb file using editconf -f spc216.pdb -o spc216.gro). Could anyone please guide me about possible issues, and how to resolve them? You're asking genbox to do far too many things at once. Divide your procedure into steps: 1. Set a box size using editconf for either the CNT or DNA. I should say a sensible box size - a 2x2x2 box barely accommodates the smallest DNA fragment, and then certainly does not leave any room at all to accommodate the minimum image convention. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] genbox output taking forever to complete
Okay, so I divided the procedure in three steps, and this does produce output immediately. But it seems that it doesn't put second molecule inside the box. Here is the what I am doing: 1. editconf -f ssgcg.pdb -o ssgcg.gro -box 20 20 20 2. genbox -cp ssgcg.gro -ci cntcapped.pdb -nmol 1 -o cntdna.gro 3. editconf -f spc216.pdb -o spc216.gro -box 20 20 20 4. genbox -cp cntdna.gro -cs spc216.gro -o solvated.gro 5. editconf -f solvated.gro -o solvated.pdb I tried cubic boxes of different lenghts (10, 20, 100), but when I see the final file in solvated.pdb in rasmol, it seems that it puts dna, and cnt at a distance equal to the specified length of the box, and the water molecules are all clustered around dna only. I also tried to create a box of lenght 100 20 20 and align dna along 1 0 0, but I still got the similar final output. My question is, what determines the distance between molecules inside the box, and how can I make sure that they are placed at a reasonable distance inside the solvent? Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sat, April 16, 2011 6:19:39 PM Subject: Re: [gmx-users] genbox output taking forever to complete Justin A. Lemkul wrote: majid hasan wrote: Dear All, I am trying to add a single strand dna, and single walled carbon nanotube in a box using the genbox command. After typing following command: genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o cntdna.gro, I get: Reading solute configuration Containing 168 atoms in 1 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration Giving Russians Opium May Alter Current Situation solvent configuration contains 648 atoms in 216 residues and then it takes forever to produce output. I tried to generate an output with just one molecule in solvent (spc216.gro), and I ran into same problem. I suspect something is wrong with my solvent input (file attached). I copied this file from gromacs/tutor/water folder, though it looks reasonable when I view I view the corresponding .pdb file in rasmol (I created .gro file from .pdb file using editconf -f spc216.pdb -o spc216.gro). Could anyone please guide me about possible issues, and how to resolve them? You're asking genbox to do far too many things at once. Divide your procedure into steps: 1. Set a box size using editconf for either the CNT or DNA. I should say a sensible box size - a 2x2x2 box barely accommodates the smallest DNA fragment, and then certainly does not leave any room at all to accommodate the minimum image convention. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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
