[gmx-users] Chemical Potential
Dear Gmx Users, I am wondering whether it is possible to obtain in Gromacs chemical potential e.g. of water in the protein - ligand system? Please, advise me to do some further reading, suggest method, maybe tutorial? Thank you, Steven -- 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] Chemical Potential
On 01/19/2012 11:34 AM, Steven Neumann wrote: Does anyone can help? Dear Gmx Users, I am wondering whether it is possible to obtain in Gromacs chemical potential e.g. of water in the protein - ligand system? Please, advise me to do some further reading, suggest method, maybe tutorial? Thank you, Steven Dear Steven I am not an expert of protein - ligand system... However the chemical potential of a i-th specie is the derivative of the potential energy in function of the number of the i-particles present in the system. As far as I know (and if I am not wrong), in GROMACS the number of particle is fixed along all the simulation, i.e., you cannot change the number of particles during the simulation. Therefore, you cannot simply obtain the chemical potential from one single run... I suggest you to search in literature; maybe you can combine different runs to obtain the chemical potential...but I do not want to say you something wrong since I do not have experience in such systems. Good luck Ivan -- -- Ivan Gladich, Ph.D. Postdoctoral Fellow Academy of Sciences of the Czech Republic Institute of Organic Chemistry and Biochemistry AS CR, v.v.i. Flemingovo nám. 2. 166 10 Praha 6 Czech Republic Tel: +420775504164 e-mail: ivan.glad...@uochb.cas.cz web page:http://www.molecular.cz/~gladich/ - -- 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-gpu error
On 19/01/2012 8:45 PM, aiswarya pawar wrote: Mark, THe normal mdrun also hangs thus not generating any output. OK. It's your problem to solve... keep simplifying stuff until you can isolate a small number of possible causes. Top of the list is file system availability. Mark On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com wrote: Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. No, but you should start trying to simplify what you're doing to see where the problem lies. Does normal mdrun work? Mark Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Pállszilard.p...@cbr.su.se mailto:szilard.p...@cbr.su.se Sender:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org Date: Wed, 18 Jan 2012 14:47:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org mailto:gmx-users@gromacs.org Reply-To: Discussion list for GROMACS usersgmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun-gpu error Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing listgmx-us...@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 togmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-us...@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive athttp://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 togmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-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 -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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] getting rid of PBC, completely
On Thu, Jan 19, 2012 at 3:49 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Chandan, The box is accessible from the t_trxframe struct. Assuming you have t_trxframe *fr You can access it through fr-box Thanks Tsjerk. It (fr.box) did help me to get the box coordinates. fr.box[XX][XX], fr.box[YY][YY] and fr.box[ZZ][ZZ] gives me the values but fr.box[XX][YY], fr.box[XX][ZZ] prints 0. Which seems to me that the origin of the box is at (0,0,0). Then, fr.box[XX][XX] is the maximum X-coordinate, fr.box[YY][YY] is the maximum Y-coordinate,fr.box[ZZ][ZZ] is the maximum Z-coordinate. Am I correct? But if you remove jumps first, you're fine anyway. Just don't put things back in the box afterwards. And don't center if your aim is calculating MSDs. Yeah, you are right. Chandan Hope it helps, Tsjerk On Thu, Jan 19, 2012 at 11:14 AM, Chandan Choudhury iitd...@gmail.com wrote: On Thu, Jan 19, 2012 at 12:17 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 5:39 PM, Chandan Choudhury wrote: Dear gmx-users, I have a simulated a system containing a linear polymer in a cubic box with water molecules. I need to get rid of PBC effect on the system such that I can execute my own analysis code. I intend to compute the msd of water molecules along the polymer backbone. You can't get rid of PBC, you can only manage it. The question reduces what you want to see if a molecule diffuses across the periodic boundary from near one end of the polymer to the other end. So, when I execute my own analysis code, I see the msd's are abrupt (i.e very high), this is due to the pbc. So, for getting rid of PBC effect, I performed the suggested trjconv workflow ( http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions ). Below are my executed commands : # Made the system whole echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o 0-4_whole.xtc # 0 is the whole system. md0-4.tpr is the initial tpr file containing whole (no broken) polymer inside the cubic box. # Extracted 1st frame from the initial trajectory echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump -o 1st.pdb -dump 0 # used the whole trajectory to remove jumps with reference to the 1st frame. echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o 0-4_nojump.xtc So here you said let molecules diffuse away from the solute. #system is being centered echo 0 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o 0-4_center.xtc -center #putting every atom in the box echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc atom ... and now you said take all the atoms and put them back in the box, creating jumps whenever one crosses the boundaries. Still when I execute my analysis code, I do see the abrupt behaviour in the msd plot. Can someone guide me how to completely get rid of PBC artifacts. Don't simulate with them :-P Is your analysis technique sound for the periodic case? No, my analysis code doesnot take care of PBC. As to deal with PBC, I need to have the box vectors (for atleast NPT simulation) from the trajectory and I am unable to extract the box vectors (as of date). Chandan 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 -- Chandan kumar Choudhury NCL, Pune INDIA -- 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 Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
Re: [gmx-users] getting rid of PBC, completely
Hi Chandan, fr.box[XX][XX], fr.box[YY][YY] and fr.box[ZZ][ZZ] gives me the values but fr.box[XX][YY], fr.box[XX][ZZ] prints 0. Which seems to me that the origin of the box is at (0,0,0). Then, fr.box[XX][XX] is the maximum X-coordinate, fr.box[YY][YY] is the maximum Y-coordinate,fr.box[ZZ][ZZ] is the maximum Z-coordinate. Am I correct? That's correct if the box is rectangular. If it's triclinic, the furthest point has (xx+yx+zx,yy+zy,zz), where xx stands for fr.box[XX][XX]. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] pdb2gmx -ter with cyclic peptide
Hi there, normally to generate a cyclic peptide I use to edit specbond.dat to force the bond between the N- and C-termini and I use the -ter flag into pdb2gmx tool in order to avoid to add hydrogens and oxygen to the end of the peptide. This was okay until the gromacs version 4.0.5 with opls ff. Now using gromacs 4.5.3 with opls ff I get this message: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. did something change or is is a bug? I have checked in the mailing list and I did not find any answer. thanks in advance for any help and -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri - -- 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] Chemical Potential
Thank you very much guys! I will search for some reading. If you can suggest a tutorial I will appreciate. On Thu, Jan 19, 2012 at 11:57 AM, René Pool r.p...@vu.nl wrote: Hi, If I understand the question correctly, you want to know the water chemical potential in the water/protein/ligand system. If so, in principle it should be possible to approximate the water chemical potential using test particle insertion. Gromacs has a utility for that. Cheers, René ==**=== René Pool Division of Molecular and Computational Toxicology Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit Amsterdam De Boelelaan 1083 1081HV AMSTERDAM, the Netherlands - IBIVU/Bioinformatics Department of Computer Science Vrije Universiteit Amsterdam De Boelelaan 1081a 1081HV AMSTERDAM, the Netherlands Room P 2.75 E: r.p...@vu.nl T: +31 20 598 76 12 F: +31 20 598 76 10 ==**=== On 01/19/2012 02:49 PM, Ivan Gladich wrote: On 01/19/2012 11:34 AM, Steven Neumann wrote: Does anyone can help? Dear Gmx Users, I am wondering whether it is possible to obtain in Gromacs chemical potential e.g. of water in the protein - ligand system? Please, advise me to do some further reading, suggest method, maybe tutorial? Thank you, Steven Dear Steven I am not an expert of protein - ligand system... However the chemical potential of a i-th specie is the derivative of the potential energy in function of the number of the i-particles present in the system. As far as I know (and if I am not wrong), in GROMACS the number of particle is fixed along all the simulation, i.e., you cannot change the number of particles during the simulation. Therefore, you cannot simply obtain the chemical potential from one single run... I suggest you to search in literature; maybe you can combine different runs to obtain the chemical potential...but I do not want to say you something wrong since I do not have experience in such systems. Good luck Ivan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Residue representation
Dear Gmx Users, I am simulating (Charmm27 ff) my protein in presence of a tube (made of atoms). This tube is a representation of a surface of protein. I want to do an approximation of residues on the surface. I divided amino acids and represent them as: - positively charged - I used Na+ [ SOD ] [ atoms ] SOD SOD 1.00 0 -negatively charged - I used CL- [ CLA ] [ atoms ] CLA CLA -1.00 0 - hydrophilic - I took Oxygen from Tyrosine OH group [ TYR ] [ atoms ] OH OH1 -0.54 13 - hydrophobic - I want to take Carbon atom - but I have no clue from which group - I guess somethin positive? Or random Carbon from hydrophobic amino acids Please, let me know your opinion for such representation. Would you suggest representing charged amino acids by atoms taken from charged amino acids (e.g. N from Arg?) Do you think its a good approximation? Thank you Steven -- 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-gpu error
And sorting out where the /bin/cat error comes from because that is surely not a Gromacs message! Cheers, -- Szilárd On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 8:45 PM, aiswarya pawar wrote: Mark, THe normal mdrun also hangs thus not generating any output. OK. It's your problem to solve... keep simplifying stuff until you can isolate a small number of possible causes. Top of the list is file system availability. Mark On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote: Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. No, but you should start trying to simplify what you're doing to see where the problem lies. Does normal mdrun work? Mark Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Páll szilard.p...@cbr.su.se Sender: gmx-users-boun...@gromacs.org Date: Wed, 18 Jan 2012 14:47:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun-gpu error Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 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 -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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
Re: [gmx-users] mdrun-gpu error
Has the tesla card got to do anything with the error. Am using Nvidia Tesla S1070 1U server. On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: And sorting out where the /bin/cat error comes from because that is surely not a Gromacs message! Cheers, -- Szilárd On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 8:45 PM, aiswarya pawar wrote: Mark, THe normal mdrun also hangs thus not generating any output. OK. It's your problem to solve... keep simplifying stuff until you can isolate a small number of possible causes. Top of the list is file system availability. Mark On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote: Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. No, but you should start trying to simplify what you're doing to see where the problem lies. Does normal mdrun work? Mark Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Páll szilard.p...@cbr.su.se Sender: gmx-users-boun...@gromacs.org Date: Wed, 18 Jan 2012 14:47:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun-gpu error Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 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 -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive
Re: [gmx-users] mdrun-gpu error
when i tired running it again, i got an error as Cuda error in file '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels// bbsort.cu' in line 176 : unspecified launch failure. /bin/cat: file_loc: No such file or directory On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote: Has the tesla card got to do anything with the error. Am using Nvidia Tesla S1070 1U server. On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: And sorting out where the /bin/cat error comes from because that is surely not a Gromacs message! Cheers, -- Szilárd On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 8:45 PM, aiswarya pawar wrote: Mark, THe normal mdrun also hangs thus not generating any output. OK. It's your problem to solve... keep simplifying stuff until you can isolate a small number of possible causes. Top of the list is file system availability. Mark On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote: Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. No, but you should start trying to simplify what you're doing to see where the problem lies. Does normal mdrun work? Mark Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Páll szilard.p...@cbr.su.se Sender: gmx-users-boun...@gromacs.org Date: Wed, 18 Jan 2012 14:47:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun-gpu error Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 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 -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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
[gmx-users] Problem with Position Restraints (before running SMD)!
Hi guys, When I did my SMD simulation by applying load to a certain group of atoms and fixing certain atoms by modifying the topology file, the points that i have fixed moved from there original position. I don't know what the problem is! Any suggestion! To make what I was doing clear, I started the equilibrium by creating a box and filling it with water. Then I did the energy minimization. After that I heated up and pressurized the structure. Every thing is good so far. After that, I modified the topology file by adding four points that i want to fix as following:; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 1 1 1000 1000 1000 13301 1000 1000 1000 - my 1st point 14261 1000 1000 1000 - my 2nd point 14371 1000 1000 1000 -my 3rd point1548 1 1000 1000 1000 -my 4th point #endifThis only what I did to fix the points. The results have shown that the fixid points moved from their original position. Here is my topology file: ; ; File '3gm1a.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Sat Jul 2 14:03:14 2011 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.3 ; ; Command line was: ; pdb2gmx -f 3gm1a.pdb -o 3gm1a.gro -p 3gm1a.top ; ; Force field data was read from: ; /opt/apps/pgi7_2/mvapich1_1_0_1/gromacs/4.5.3/share/gromacs/top ; ; Note: ; This might be a non-standard force field location. When you use this topology, the ; force field must either be present in the current directory, or the location ; specified in the GMXLIB path variable or with the 'include' mdp file option. ; ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include 3gm1a_Protein_chain_A.itp #include 3gm1a_Protein_chain_E.itp #include 3gm1a_Protein_chain_F.itp ; Include water topology #include gromos53a6.ff/spc.itp#ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 13301 1000 1000 1000 14261 1000 1000 1000 14371 1000 1000 1000 15481 1000 1000 1000 #endif ; Include topology for ions #include gromos53a6.ff/ions.itp [ system ]; Name PROTEIN TYROSINE KINASE 2 BETA; 5 RESIDUES 861-1009; PAXILLIN in water [ molecules ]; Compound#mols Protein_chain_A 1 Protein_chain_E 1 Protein_chain_F 1 SOL 8788 NA 25 CL 18 And Here is my mdp file: title = smd_120 ; 120 pN ; this is loosely based off of the VT pulling tutorial; heavily modified ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250 ; 5 ns ; Output parameters nstxout = 1000 ; every 2 ps nstvout = 1000 nstfout = 5000 nstxtcout = 5000 ; every ps nstenergy = 1000 ; Bond parameters constraint_algorithm= lincs constraints = hbonds lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.16 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.2 0.2 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; COM motion removal ; These options remove comm motion of the constraint / freeze group nstcomm = 1 comm_mode = Linear comm_grps = System ; pull parameters pull= constant_force pull_geometry = direction pull_nstxout= 500 ; will print the c.o.m. coordinates pull_nstfout= 500 ; forces on group pull_ngroups= 1 pull_group0 = Protein ; pull_group1 = group_B ; pull_pbcatom1 = 100 ; the CA of the 10th residue pull_vec1 = -2.63 -16.48 -14.95 ; direction of pull, will be normalized pull_k1 = 72.29 ; pull_k1*1.66 = pN; units: [kJ / (mol * nm^2)] What should I do? Thanks,Talal -- gmx-users mailing list
Re: [gmx-users] Problem with Position Restraints (before running SMD)!
Talal E. AlOtaibi wrote: Hi guys, When I did my SMD simulation by applying load to a certain group of atoms and fixing certain atoms by modifying the topology file, the points that i have fixed moved from there original position. I don't know what the problem is! Any suggestion! Position restraints disfavor motion, they don't prevent it. If the pulling force is sufficient to overcome the restraint bias, then the atoms move. Two options: 1. Use a stronger position restraint force constant 2. Use freezegrps instead - these don't move -Justin To make what I was doing clear, I started the equilibrium by creating a box and filling it with water. Then I did the energy minimization. After that I heated up and pressurized the structure. Every thing is good so far. After that, I modified the topology file by adding four points that i want to fix as following: ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 1 1 1000 1000 1000 1330 1 1000 1000 1000 - my 1st point 1426 1 1000 1000 1000 - my 2nd point 1437 1 1000 1000 1000 - my 3rd point 1548 1 1000 1000 1000 - my 4th point #endif This only what I did to fix the points. The results have shown that the fixid points moved from their original position. Here is my topology file: ; ; File '3gm1a.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Sat Jul 2 14:03:14 2011 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.3 ; ; Command line was: ; pdb2gmx -f 3gm1a.pdb -o 3gm1a.gro -p 3gm1a.top ; ; Force field data was read from: ; /opt/apps/pgi7_2/mvapich1_1_0_1/gromacs/4.5.3/share/gromacs/top ; ; Note: ; This might be a non-standard force field location. When you use this topology, the ; force field must either be present in the current directory, or the location ; specified in the GMXLIB path variable or with the 'include' mdp file option. ; ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include 3gm1a_Protein_chain_A.itp #include 3gm1a_Protein_chain_E.itp #include 3gm1a_Protein_chain_F.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 13301 1000 1000 1000 14261 1000 1000 1000 14371 1000 1000 1000 15481 1000 1000 1000 #endif ; Include topology for ions #include gromos53a6.ff/ions.itp [ system ] ; Name PROTEIN TYROSINE KINASE 2 BETA; 5 RESIDUES 861-1009; PAXILLIN in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_E 1 Protein_chain_F 1 SOL 8788 NA 25 CL 18 And Here is my mdp file: title = smd_120 ; 120 pN ; this is loosely based off of the VT pulling tutorial; heavily modified ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250 ; 5 ns ; Output parameters nstxout = 1000 ; every 2 ps nstvout = 1000 nstfout = 5000 nstxtcout = 5000 ; every ps nstenergy = 1000 ; Bond parameters constraint_algorithm= lincs constraints = hbonds lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.16 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.2 0.2 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; COM motion removal ; These options remove comm motion of the constraint / freeze group nstcomm = 1 comm_mode = Linear comm_grps = System ; pull parameters pull= constant_force pull_geometry = direction pull_nstxout= 500 ; will print the c.o.m. coordinates pull_nstfout= 500 ; forces on group pull_ngroups= 1 pull_group0 = Protein ; pull_group1 = group_B ; pull_pbcatom1 = 100 ; the CA of the 10th
[gmx-users] How to find Hbonding partner
Hi, I am wondering whether there is any way in GROMACS that one can find which groups are the main Hbonding partners in a trajectory. For example, if I simulate a peptide in water, I want to know during the simulation, which particular atoms in the peptides are making most of the Hbonds with water as a function of time. I find g_hbond can tell us the total number of Hbond between two groups as a function of time but, can it specify which groups are making the Hbonds most of the time ? Any help will be appreciated. Sanku-- 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] writing checkpoints
We are running quite a large system with a default checkpoint intervals (15 minutes). However, in the md.log file, it is written like below Writing checkpoint, step 138 at Thu Jan 19 11:00:36 2012 Writing checkpoint, step 1380010 at Thu Jan 19 11:00:41 2012 Writing checkpoint, step 1380020 at Thu Jan 19 11:00:46 2012 Writing checkpoint, step 1380030 at Thu Jan 19 11:00:51 2012 Writing checkpoint, step 1380040 at Thu Jan 19 11:00:55 2012 Writing checkpoint, step 1380050 at Thu Jan 19 11:01:00 2012 Then after an hour - Writing checkpoint, step 139 at Thu Jan 19 12:21:18 2012 Writing checkpoint, step 1390010 at Thu Jan 19 12:21:23 2012 Writing checkpoint, step 1390020 at Thu Jan 19 12:21:28 2012 Writing checkpoint, step 1390030 at Thu Jan 19 12:21:32 2012 The job is executed using 4 cores. The version is 4-0-7. Is this a bug? Just curious. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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-gpu error
That's a generic GPU kernel launch failure which can mean anything, from faulty hardware to bad driver to messed up installation. Does the memory test run? Try to compile/install again and see if it works. -- Szilárd On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: when i tired running it again, i got an error as Cuda error in file '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//bbsort.cu' in line 176 : unspecified launch failure. /bin/cat: file_loc: No such file or directory On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Has the tesla card got to do anything with the error. Am using Nvidia Tesla S1070 1U server. On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: And sorting out where the /bin/cat error comes from because that is surely not a Gromacs message! Cheers, -- Szilárd On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 8:45 PM, aiswarya pawar wrote: Mark, THe normal mdrun also hangs thus not generating any output. OK. It's your problem to solve... keep simplifying stuff until you can isolate a small number of possible causes. Top of the list is file system availability. Mark On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote: Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. No, but you should start trying to simplify what you're doing to see where the problem lies. Does normal mdrun work? Mark Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Páll szilard.p...@cbr.su.se Sender: gmx-users-boun...@gromacs.org Date: Wed, 18 Jan 2012 14:47:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun-gpu error Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 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 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 -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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?
Re: [gmx-users] mdrun-gpu error
Szilárd, I did a memory test run yesterday and it went fine but today received an error. So you mean to say the tesla card version nothing to do with this right. Thanks On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: That's a generic GPU kernel launch failure which can mean anything, from faulty hardware to bad driver to messed up installation. Does the memory test run? Try to compile/install again and see if it works. -- Szilárd On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: when i tired running it again, i got an error as Cuda error in file '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels// bbsort.cu' in line 176 : unspecified launch failure. /bin/cat: file_loc: No such file or directory On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Has the tesla card got to do anything with the error. Am using Nvidia Tesla S1070 1U server. On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: And sorting out where the /bin/cat error comes from because that is surely not a Gromacs message! Cheers, -- Szilárd On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 8:45 PM, aiswarya pawar wrote: Mark, THe normal mdrun also hangs thus not generating any output. OK. It's your problem to solve... keep simplifying stuff until you can isolate a small number of possible causes. Top of the list is file system availability. Mark On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote: Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. No, but you should start trying to simplify what you're doing to see where the problem lies. Does normal mdrun work? Mark Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Páll szilard.p...@cbr.su.se Sender: gmx-users-boun...@gromacs.org Date: Wed, 18 Jan 2012 14:47:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun-gpu error Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol option. /bin/cat: file_loc: No such file or directory and the job is running but the nothing written into .xtc, .trr, .edr files . What could have gone wrong? -- Aiswarya B Pawar Bioinformatics Dept, Indian Institute of Science Bangalore -- 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 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-gpu error
aiswarya pawar wrote: Szilárd, I did a memory test run yesterday and it went fine but today received an error. So you mean to say the tesla card version nothing to do with this right. You're trying to solve multiple problems at once. You told Mark that the normal mdrun executable (which works independently of any GPU components) also hangs, so either your filesystem is faulty or your installation procedure produced nonfunctional executables. You're posting bits and pieces of information, which makes it incredibly hard for anyone to help you. Let's recap and try again. Please provide: 1. The Gromacs version you're using 2. Description of the hardware (GPU and non-GPU components) 3. Installation procedure for Gromacs and any of the prerequisite software and libraries that were required, including versions 4. The exact command(s) you're issuing, including the full script that is causing a problem -Justin Thanks On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll szilard.p...@cbr.su.se mailto:szilard.p...@cbr.su.se wrote: That's a generic GPU kernel launch failure which can mean anything, from faulty hardware to bad driver to messed up installation. Does the memory test run? Try to compile/install again and see if it works. -- Szilárd On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com wrote: when i tired running it again, i got an error as Cuda error in file '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//bbsort.cu http://bbsort.cu' in line 176 : unspecified launch failure. /bin/cat: file_loc: No such file or directory On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com wrote: Has the tesla card got to do anything with the error. Am using Nvidia Tesla S1070 1U server. On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll szilard.p...@cbr.su.se mailto:szilard.p...@cbr.su.se wrote: And sorting out where the /bin/cat error comes from because that is surely not a Gromacs message! Cheers, -- Szilárd On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 19/01/2012 8:45 PM, aiswarya pawar wrote: Mark, THe normal mdrun also hangs thus not generating any output. OK. It's your problem to solve... keep simplifying stuff until you can isolate a small number of possible causes. Top of the list is file system availability. Mark On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com wrote: Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. No, but you should start trying to simplify what you're doing to see where the problem lies. Does normal mdrun work? Mark Thanks Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Páll szilard.p...@cbr.su.se mailto:szilard.p...@cbr.su.se Sender: gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org Date: Wed, 18 Jan 2012 14:47:59 To: Discussion list for GROMACS usersgmx-users@gromacs.org mailto:gmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun-gpu error Hi, Most of those are just warnings, the only error I see there comes from the shell, probably an error in your script. Cheers, -- Szilárd On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com wrote: Hi users, Am running mdrun on gpu . I receive an error such as= WARNING: This run will generate roughly 38570 Mb of data WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.
[gmx-users] Reg: Number of nodes in REMD
Hi there, I am trying to run REMD using the following command mdrun_mpi -s run_.tpr -multi 8 -replex 100 and i am getting the following error Fatal error: The number of nodes (1) is not a multiple of the number of simulations (8) i tried using -np option to give the number of nodes but it is also not working. I installed gromacs_mpich using synaptics in ubuntu. Any help please. Thanks Rohit -- Rohit Farmer PhD Biosciences (2011-2014) Center for Systems Biology University of Birmingham Birmingham B152TT United Kingdom Email : rohit.far...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reg: Number of nodes in REMD
Rohit Farmer wrote: Hi there, I am trying to run REMD using the following command mdrun_mpi -s run_.tpr -multi 8 -replex 100 and i am getting the following error Fatal error: The number of nodes (1) is not a multiple of the number of simulations (8) i tried using -np option to give the number of nodes but it is also not working. The mdrun_mpi -np option is not used; the parallel job needs to be initiated via mpirun, e.g.: mpirun -np 8 mdrun_mpi ... Otherwise, install Gromacs yourself to make use of threading rather than MPI. -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] sudden jumps in RMSD etc.
Hi all, I am doing duplicate MD simulations with a protein-ligand system. After processing one trajectory by trjconv with the optioin -pbc nojump, I still find abrupt jumps (on the scale of nm) in RMSDs and COM distances. Then I tried -pbc mol -ur compact, which did not work. And then -fit progressive on protein atoms, which again did not completely eliminate those jumps in protein atom RMSDs. I wonder if I have not used the right option? Thanks for any advice, Yun -- 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] query on g_sorient
Hi, I am trying to understand what are the angles g_sorient plans to compute. The manual says that the theta1 is the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3 . But, I wonder what is the reference position of this angle ? In other words, what is the 3rd atom that one needs for the calculation angle ( the first atom being the water-oxygen, second atom being the midpoint of two water-hydrogen) ? Is the 3rd atom any solute atom or their center of mass ? Thanks Sanku-- 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] sudden jumps in RMSD etc.
On 20/01/2012 7:55 AM, Yun Shi wrote: Hi all, I am doing duplicate MD simulations with a protein-ligand system. After processing one trajectory by trjconv with the optioin -pbc nojump, I still find abrupt jumps (on the scale of nm) in RMSDs and COM distances. Then I tried -pbc mol -ur compact, which did not work. And then -fit progressive on protein atoms, which again did not completely eliminate those jumps in protein atom RMSDs. I wonder if I have not used the right option? There's a suggested workflow here http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions which you can adapt to your needs. 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] Lincs warnings
On 20/01/12, Ben Porebski b...@inoxx.net wrote: Hi all, I've been working on some structures between 2.5A and 3.4A in resolution and all of my structures suffer from lincs warnings. From reading the page about lincs warnings, I've performed a more lengthy equilibration: I'm using gromacs 4.0.7 single precision and the G53a6 force field with spc water model. - Genbox, add ions. - EM until converges - Positional restraints at 2,000 kJ/mol, 200, 20 and 2 for 100ps each at 100K - Followed by simulated annealing with the following parameters: ; Simulated annealing @ positional restraint of 2 kJ/mol annealing = single single annealing_npoints = 3 3 annealing_time = 0 50 2500 50 250 annealing_temp = 100 100 300 100 100 300 - This then undergoes 750ps of md at 300K. Once done. I continue the run in my production MD. Sometimes my structures will crash within 5 ns, sometimes it will run out for 60 ns before I start seeing any lincs warnings. An important trouble-shooting stage is to observe in a visualization program what happens in your simulation immediately before a crash, and look also at the variation in the energy terms. That might mean saving output more often. This could clue you in to a region of structure that is problematic, either atomic clashes that persist through EM+SA, or a malformed topology. See http://www.gromacs.org/Documentation/Terminology/Blowing_Up. Note also that restraining atoms to positions that are of low resolution can be problematic - you apparently don't want large rearrangements during equilibration, but it seems you need to permit more. Note what grompp -h has to say about position restraints. I've attempted to further refine the structures and they behave a little better, but still crash, just less often. To continue the simulation, I will not use the .trr output from the previous simulation. If this doesn't work, I'll run the simulation using shake for 2 ns, but this is significantly slower. I'm a little concerned that these crashes may be introducing some sort of error into the simulation and I'm not sure of the right way to get around this problem. I've played around with changing the lincs order and lincs iteration parameters, which appear to reduce the number of lincs warnings and slows down the simulation slightly. The constraint algorithms are normally not the problem, they're just the machinery most prone to breaking when something else goes wrong. As such, tweaking them is not productive. Another thing I've played with was the constraints. Changing this from all-bonds to hbonds. This stopped my crashes, but a co-worker thought that it may not be accurately modelling the system, or would introduce anomalies into the simulation. My impression was that changing from all-bonds to hbonds would improve the accuracy of the system... But I could be wrong. The accuracy of the numerical integration is strongly tied to the size of the time step and the kinds of constraints you are using. See manual section 6.5. One strategy in your case is a lengthy equilibration period with a short time step (say 0.5fs) and no constraints or restraints at all. Monitor the trends in the energy terms over this period to see if changes are occurring. Mark If anyone has experience with dealing with lincs warnings or simulating low resolution structures, help would be amazing. I've been stuck on this for quite some time now. Cheers, Ben -- 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-gpu error
Justin, Sorry for not giving the correct information. Gromacs version 4.5.5 Tesla card- Nvidia Tesla S1070 (Tesla T10 Processor) Cuda version 3.1 CMake 2.8 I installed the OpenMM from the source using commands= ccmake -i . make make test make install everything went fine and set the paths export OPENMM_ROOT_DIR=path_to_custom_openmm_installation cmake -DGMX_OPENMM=ON then make make install The submission script used is= #!/bin/csh #PBS -l gpu=1 #PBS -l ncpus=1 #PBS -o /global/utemp/cuda-out2.out #PBS -e /global/utemp/cuda-err2.out /home/staff/software/gromacs_gpu_t/bin/mdrun-gpu -device OpenMM:platform=Cuda,DeviceID=0,Memtest=15,**,force-device=yes -v -deffnm /global/utemp/md for this i receive an error such as Cuda error in file '/home/staff/software/openmm_tesla/platforms/cuda/./src/kernels//bbsort.cu' in line 176 : unspecified launch failure. /bin/cat: file_loc: No such file or directory On Thu, Jan 19, 2012 at 11:41 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya pawar wrote: Szilárd, I did a memory test run yesterday and it went fine but today received an error. So you mean to say the tesla card version nothing to do with this right. You're trying to solve multiple problems at once. You told Mark that the normal mdrun executable (which works independently of any GPU components) also hangs, so either your filesystem is faulty or your installation procedure produced nonfunctional executables. You're posting bits and pieces of information, which makes it incredibly hard for anyone to help you. Let's recap and try again. Please provide: 1. The Gromacs version you're using 2. Description of the hardware (GPU and non-GPU components) 3. Installation procedure for Gromacs and any of the prerequisite software and libraries that were required, including versions 4. The exact command(s) you're issuing, including the full script that is causing a problem -Justin Thanks On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll szilard.p...@cbr.su.semailto: szilard.p...@cbr.su.se** wrote: That's a generic GPU kernel launch failure which can mean anything, from faulty hardware to bad driver to messed up installation. Does the memory test run? Try to compile/install again and see if it works. -- Szilárd On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar aiswarya.pa...@gmail.com mailto:aiswarya.pawar@gmail.**comaiswarya.pa...@gmail.com wrote: when i tired running it again, i got an error as Cuda error in file '/home/staff/sec/secdpal/**software/openmm_tesla/** platforms/cuda/./src/kernels//**bbsort.cu http://bbsort.cu http://bbsort.cu' in line 176 : unspecified launch failure. /bin/cat: file_loc: No such file or directory On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar aiswarya.pa...@gmail.com mailto:aiswarya.pawar@gmail.**comaiswarya.pa...@gmail.com wrote: Has the tesla card got to do anything with the error. Am using Nvidia Tesla S1070 1U server. On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll szilard.p...@cbr.su.se mailto:szilard.p...@cbr.su.se** wrote: And sorting out where the /bin/cat error comes from because that is surely not a Gromacs message! Cheers, -- Szilárd On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.**aumark.abra...@anu.edu.au wrote: On 19/01/2012 8:45 PM, aiswarya pawar wrote: Mark, THe normal mdrun also hangs thus not generating any output. OK. It's your problem to solve... keep simplifying stuff until you can isolate a small number of possible causes. Top of the list is file system availability. Mark On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.**aumark.abra...@anu.edu.au wrote: On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com mailto:aiswarya.pawar@gmail.**com aiswarya.pa...@gmail.com wrote: Hi, Its going into the running mode but gets hang there for long hours which generating any data in the output file. And am not able to figure out the error file_doc. Please anyone knows what's going wrong. No, but you should start trying to simplify what you're doing to see where the problem lies. Does normal mdrun work? Mark Thanks Sent from my BlackBerryŽ on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Szilárd Páll szilard.p...@cbr.su.se mailto:szilard.p...@cbr.su.se** Sender: gmx-users-boun...@gromacs.org
[gmx-users] Regarding ngmx with double precision
Dear All, While installing Gromacs in double precision, I am not able to make ngmx run. Is it because of lack of X libraries. I want to run ngmx trajectory viewer. So I kindly request you to suggest me to make ngmx run. Thank you in Advance *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- 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 balance charge for modeling N2 molecules
Hi, I asked this question before. Thanks to Justin, he did reply as follows. Kiwoong Kim wrote: Hi, I'm getting better to use Gromacs owing to many posts on this sites :) . I have several questions about adding the counter-ions. My system has a number of N2 molecules which has charge, -0.40484(for single N) X 2. Thus, I have to add some counter-ions to make the system neutral. However, because I'm newbie on Gromacs, I thought of several clumsy ways myself. #1. Add virtual sites (virtual atoms) which has counter-ions like below. [ atomtypes ] ; name mass charge ptype sigma epsilon DUM 00.80968 V0.00.0 I set the coordinates of each virtual DUM atoms to the center of N2 molecules. #2. using genion in Gromacs. But, I have no idea on this. What molecules do I have to designate to charge plus ion using genion ?? I typed below line. genion -s md_0_1.tpr -n index.ndx -o ton_genion.pdb -g md_0_1_genion.log -p topol_genion.top -np 322 -pname dum -pq 0.80968 and selected N2 molecules which is diffusing particle. It results that the name of half of N2 molecules is changed as DUM. (maybe the system become neutral) The number of N2 molecules should be fixed. Do I have additional N2 molecule for charging using genion?? Then, what are the initial coordinates??? please help me any advises would be helpful. How can I do that??? I see no reason why you should do either. For dinitrogen, which has no net dipole, it seems intuitive to me that both N atoms should have zero charge. -Justin I made linear rigid model (CO2) by introducing virtual interaction. However, I have troubles in modelling N2 molecules. I want to model N2 with quadrupole moment according to the paper (Adsorption (2007) 13: 469-476). In the paper, the charge N2 model (originally developed by Murthy et al. (1980) can be described as follows. N (-0.40484), Dummy (N2, +0.80968). Actually, I don't know how to model N2 molecules with dummy. Please let me know any advises. Thx. Have a great day. :) -- 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] Regarding ngmx with double precision
On 20/01/2012 5:05 PM, Ravi Kumar Venkatraman wrote: Dear All, While installing Gromacs in double precision, I am not able to make ngmx run. Is it because of lack of X libraries. I want to run ngmx trajectory viewer. So I kindly request you to suggest me to make ngmx run. You need X libraries and headers, and maybe Motif/Lesstif also. I forget the details. Do search the archives. 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] How to balance charge for modeling N2 molecules
On 20/01/2012 5:51 PM, Kiwoong Kim wrote: Hi, I asked this question before. Thanks to Justin, he did reply as follows. Kiwoong Kim wrote: Hi, I'm getting better to use Gromacs owing to many posts on this sites :) . I have several questions about adding the counter-ions. My system has a number of N2 molecules which has charge, -0.40484(for single N) X 2. Thus, I have to add some counter-ions to make the system neutral. However, because I'm newbie on Gromacs, I thought of several clumsy ways myself. #1. Add virtual sites (virtual atoms) which has counter-ions like below. [ atomtypes ] ; name mass charge ptype sigma epsilon DUM 00.80968 V0.00.0 I set the coordinates of each virtual DUM atoms to the center of N2 molecules. #2. using genion in Gromacs. But, I have no idea on this. What molecules do I have to designate to charge plus ion using genion ?? I typed below line. genion -s md_0_1.tpr -n index.ndx -o ton_genion.pdb -g md_0_1_genion.log -p topol_genion.top -np 322 -pname dum -pq 0.80968 and selected N2 molecules which is diffusing particle. It results that the name of half of N2 molecules is changed as DUM. (maybe the system become neutral) The number of N2 molecules should be fixed. Do I have additional N2 molecule for charging using genion?? Then, what are the initial coordinates??? please help me any advises would be helpful. How can I do that??? I see no reason why you should do either. For dinitrogen, which has no net dipole, it seems intuitive to me that both N atoms should have zero charge. -Justin I made linear rigid model (CO2) by introducing virtual interaction. However, I have troubles in modelling N2 molecules. I want to model N2 with quadrupole moment according to the paper (Adsorption (2007) 13: 469-476). In the paper, the charge N2 model (originally developed by Murthy et al. (1980) can be described as follows. N (-0.40484), Dummy (N2, +0.80968). Right... that's totally different from N2 with charged N atoms :) Actually, I don't know how to model N2 molecules with dummy. Please let me know any advises. Sounds like virtual site type 2 is perfect - and didn't you already use that for CO2? See section 4.7 and somewhere in chapter 5. Mark Thx. Have a great day. :) -- 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
