[gmx-users] ApoA1 benchmark or reading CHARMM topologies in gromacs
Hi, Short summary: Is there a gromacs version of the NAMD ApoA1 benchmark somewhere and if not, what tools can I use to convert CHARMM parameter/topology files to gromacs? Now for the long version: I'm currently trying to port the popular ApoA1 benchmark used by NAMD and Desmond to gromacs. I have the input files for NAMD (they can be downloaded from http://www.ks.uiuc.edu/Research/namd/utilities/apoa1/), i.e. a PDB and PSF file as well as the corresponding .xplor force-field parameter files. I also have the underlying CHARMM topology files for the lipids involved. I've tried generating gromacs input files using pdb2gmx, using the CHARMM27 force-field therein. This doesn't work due to an Atom OXT in residue GLN 243 was not found error which seems to be an occurrence of bug #567 (http://redmine.gromacs.org/issues/567), yet it can't be circumvented by replacing the type of of the OT2 atom. I tried using the OPLS force field instead (after replacing HSD with HIS and other minor modifications in the .pdb), but this fails with the same error as above. If I don't include chain ids in the pdb, then it fails since it does not recognize the POPC lipid residues. I have the CHARMM topology files for these, but I have no idea how to convert these to gromacs topologies. Now, since the ApoA1 benchmark is quite popular, I'm assuming somebody might already have a gromacs version out there... Is this the case? If not, Is there some tool to convert CHARMM input, i.e. parameters and topologies, to gromacs? I've found and successfully used Mark Abraham's Perl script to convert the parameters. Therein he refers to a script by Yuguang Mu to convert topologies, which apparently used to be on the gromacs site (http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz), but which seems to have disappeared. Many thanks and kind regards, Pedro Gonnet -- 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] Doubt about HSD and HSE conformation on Charmm27
Hi, Firstly, thanks for your help Justin. You have already told me about the use of -ighn option. However, I've looked for an automatic way which managed the HIS protonation states. Unfortunatelly, I understood wrong about this algorithm. I believed that the difference about HSD and HSE was the names of atom. Now, I use -ighn option in my algorithm. It is working fine until now. This mess is because this structure is one of initial individuals. I'm working with an evolutionary algorithm. The final output is better. I have been trying to improve it. Thanks in advance, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes - http://lattes.cnpq.br/1025157978990218 Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5 On Tue, Sep 27, 2011 at 2:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: Rodrigo Faccioli wrote: Hi, I have a doubt about HIS protonation state for chamm27 force field implemented at Gromacs. I'm a computer scientist trying to understand about protein world. So, my mistakes about protein my apologies. I have been developing a program which reads a fasta file and builds a protein (3D representation) based on its internal coordinates (dihedral angles representation). This internal coordinates are based on two libraries: CADDB 2.0 and Tuffery. The algorithm which transform internal coordinates to cartesian coordinates (3D) is Nerf. Details about my project you can find at [1]. I'm using Gromacs 4.5.4. I have already started a discussion about this topic. In [2] I show Justin answer. I understood that HSD and HSE state are based on an Gromacs algorithm which choose HIS conformation HSD or HSE. I read pdb2gmx file and I found set_histp function. Furthermore, I compared these conformations on aminoacids.rtp. I seen that HSE conformation has HE2 atom instead of HD1 atom. Therefore, I understood that if the conformation contains the HD1 atom, it wiil be a HSD conformation and not HSE conformation. This is incorrect. Within pdb2gmx, histidine protonation is set based on an algorithm that searches for hydrogen bonds. The position of those hydrogen bond acceptors dictates which form (delta protonated, HSD, or epsilon protonated, HSE) is chosen. Neither naming nor the presence of certain H atoms can override the algorithm. Therefore I ran pdb2gmx to obtain the Hydrogen atoms is considered by Gromacs. I use the command below: /usr/local/gromacs/bin/./**pdb2gmx -f /home/faccioli/Execute/EESC_**AE/1BDD/PROT_HIS.pdb -o /home/faccioli/Execute/EESC_**AE/1BDD/prot_sys.pdb -ff charmm27 -water spc -p /home/faccioli/Execute/EESC_**AE/1BDD/teste.top -ignh In residue 19 at prot_sys.pdb there is HD1. So, HIS conformation must be HSD. However, when I run the command below: /usr/local/gromacs/bin/./**pdb2gmx -f /home/faccioli/Execute/EESC_**AE/1BDD/PROT_IND_0.pdb -o /home/faccioli/Execute/EESC_**AE/1BDD/prot_sys.gro -ff charmm27 -water spc -p /home/faccioli/Execute/EESC_**AE/1BDD/prot_sys.top shows a error message: Fatal error: Atom HD1 in residue HIS 19 was not found in rtp entry HSE with 17 atoms while sorting atoms. I can't understand why HSE is appeared. I appreciate any help. pdb2gmx has decided that this histidine should be epsilon protonated, and therefore the proton at the N-delta position is extraneous. Either run pdb2gmx with the -ignh option to remove all H atoms from the input and have them regenerated according to what Gromacs expects, or use the -his flag to manually choose the protonation state you want. I believe I suggested this before. All files used for my commands can be found at [3-4]. [1] https://gitorious.org/**protpred-gromacs/protpred-**gromacshttps://gitorious.org/protpred-gromacs/protpred-gromacs [2] http://lists.gromacs.org/**pipermail/gmx-users/2011-** August/063821.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2011-August/063821.html [3] http://dl.dropbox.com/u/**4270818/PROT_HIS.pdbhttp://dl.dropbox.com/u/4270818/PROT_HIS.pdb I took a look at this file; its format is still incorrect and displays as a complete mess in VMD. If you get pdb2gmx running, the output coordinate file will be similarly mangled, or worse. -Justin [4] http://dl.dropbox.com/u/**4270818/prot_sys.pdbhttp://dl.dropbox.com/u/4270818/prot_sys.pdb Thanks in advance, -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department of Electrical Engineering - SEL Intelligent System in Structure Bioinformatics http://laips.sel.eesc.usp.br Phone: 55 (16) 3373-9366 Ext 229 Curriculum Lattes -
Re: [gmx-users] ApoA1 benchmark or reading CHARMM topologies in gromacs
On 28/09/2011 6:16 PM, Pedro Gonnet wrote: Hi, Short summary: Is there a gromacs version of the NAMD ApoA1 benchmark somewhere and if not, what tools can I use to convert CHARMM parameter/topology files to gromacs? If either exists, I don't know about it. Now for the long version: I'm currently trying to port the popular ApoA1 benchmark used by NAMD and Desmond to gromacs. I have the input files for NAMD (they can be downloaded from http://www.ks.uiuc.edu/Research/namd/utilities/apoa1/), i.e. a PDB and PSF file as well as the corresponding .xplor force-field parameter files. I also have the underlying CHARMM topology files for the lipids involved. I've tried generating gromacs input files using pdb2gmx, using the CHARMM27 force-field therein. This doesn't work due to an Atom OXT in residue GLN 243 was not found error which seems to be an occurrence of bug #567 (http://redmine.gromacs.org/issues/567), yet it can't be circumvented by replacing the type of of the OT2 atom. A possible work-around is to copy residuetypes.dat to your working directory and append POPC Lipid to it. I expect this will inhibit the mechanism responsible for the unwelcome atom renaming. Please let us know if so. Alternatively, I believe another work-around is to follow the general procedure here http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, modifying the various parts of the POPC residue entry in the .rtp file to have atom names other than O1 and O2, and the PDB atom names to match. Mark I tried using the OPLS force field instead (after replacing HSD with HIS and other minor modifications in the .pdb), but this fails with the same error as above. If I don't include chain ids in the pdb, then it fails since it does not recognize the POPC lipid residues. I have the CHARMM topology files for these, but I have no idea how to convert these to gromacs topologies. Now, since the ApoA1 benchmark is quite popular, I'm assuming somebody might already have a gromacs version out there... Is this the case? If not, Is there some tool to convert CHARMM input, i.e. parameters and topologies, to gromacs? I've found and successfully used Mark Abraham's Perl script to convert the parameters. Therein he refers to a script by Yuguang Mu to convert topologies, which apparently used to be on the gromacs site (http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz), but which seems to have disappeared. Many thanks and kind regards, Pedro Gonnet -- 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] non interactive command
Hi users, I have n number of program to run so my index file is huge, i want to know if i use the command option g_energy -flags choice.txt , it takes up the numbers given right? but if i have n numbers in the choice txt. how would it take in each run , ie it will take 1st two numbers and what about the rest? Thanks -- 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] non interactive command
aiswarya pawar wrote: Hi users, I have n number of program to run so my index file is huge, i want to know if i use the command option g_energy -flags choice.txt , it takes up the numbers given right? but if i have n numbers in the choice txt. how would it take in each run , ie it will take 1st two numbers and what about the rest? You should only provide the chosen number(s), otherwise the program will try to read all of them. In the case where you have many different programs to run, it is vastly easier to run, for instance: echo x y | g_program -flags -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] non interactive command
justin, if i use echo command then i need to run again and again for each selection right? how can i run as whole bunch. Thanks On Wed, Sep 28, 2011 at 10:31 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya pawar wrote: Hi users, I have n number of program to run so my index file is huge, i want to know if i use the command option g_energy -flags choice.txt , it takes up the numbers given right? but if i have n numbers in the choice txt. how would it take in each run , ie it will take 1st two numbers and what about the rest? You should only provide the chosen number(s), otherwise the program will try to read all of them. In the case where you have many different programs to run, it is vastly easier to run, for instance: echo x y | g_program -flags -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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
Re: [gmx-users] non interactive command
aiswarya pawar wrote: justin, if i use echo command then i need to run again and again for each selection right? how can i run as whole bunch. I don't understand your question. You can write a trivial shell script for all of your analysis, e.g.: #!/bin/bash echo 4 4 | g_rms -f traj.xtc -s topol.tpr echo 1 | g_gyrate -f traj.xtc -s topol.tpr (etc) -Justin Thanks On Wed, Sep 28, 2011 at 10:31 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: aiswarya pawar wrote: Hi users, I have n number of program to run so my index file is huge, i want to know if i use the command option g_energy -flags choice.txt , it takes up the numbers given right? but if i have n numbers in the choice txt. how would it take in each run , ie it will take 1st two numbers and what about the rest? You should only provide the chosen number(s), otherwise the program will try to read all of them. In the case where you have many different programs to run, it is vastly easier to run, for instance: echo x y | g_program -flags -Justin -- ==__== 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 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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 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 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] non interactive command
i have N number of selection ie it should run as a batch. like its should select group1: 0 and select group2: 32, this is 1st run then after this next run should be select group1: 1 and select group2: 32 and so on. On Wed, Sep 28, 2011 at 10:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya pawar wrote: justin, if i use echo command then i need to run again and again for each selection right? how can i run as whole bunch. I don't understand your question. You can write a trivial shell script for all of your analysis, e.g.: #!/bin/bash echo 4 4 | g_rms -f traj.xtc -s topol.tpr echo 1 | g_gyrate -f traj.xtc -s topol.tpr (etc) -Justin Thanks On Wed, Sep 28, 2011 at 10:31 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: aiswarya pawar wrote: Hi users, I have n number of program to run so my index file is huge, i want to know if i use the command option g_energy -flags choice.txt , it takes up the numbers given right? but if i have n numbers in the choice txt. how would it take in each run , ie it will take 1st two numbers and what about the rest? You should only provide the chosen number(s), otherwise the program will try to read all of them. In the case where you have many different programs to run, it is vastly easier to run, for instance: echo x y | g_program -flags -Justin -- ==**__== 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/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://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-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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
Re: [gmx-users] non interactive command
aiswarya pawar wrote: i have N number of selection ie it should run as a batch. like its should select group1: 0 and select group2: 32, this is 1st run then after this next run should be select group1: 1 and select group2: 32 and so on. So enclose the call to the program in a for-loop in a script, echoing variables as necessary. -Justin On Wed, Sep 28, 2011 at 10:56 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: aiswarya pawar wrote: justin, if i use echo command then i need to run again and again for each selection right? how can i run as whole bunch. I don't understand your question. You can write a trivial shell script for all of your analysis, e.g.: #!/bin/bash echo 4 4 | g_rms -f traj.xtc -s topol.tpr echo 1 | g_gyrate -f traj.xtc -s topol.tpr (etc) -Justin Thanks On Wed, Sep 28, 2011 at 10:31 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: aiswarya pawar wrote: Hi users, I have n number of program to run so my index file is huge, i want to know if i use the command option g_energy -flags choice.txt , it takes up the numbers given right? but if i have n numbers in the choice txt. how would it take in each run , ie it will take 1st two numbers and what about the rest? You should only provide the chosen number(s), otherwise the program will try to read all of them. In the case where you have many different programs to run, it is vastly easier to run, for instance: echo x y | g_program -flags -Justin -- ==== 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 http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-request@__gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists 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 http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin 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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT
[gmx-users] REMD problem
Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. -- Best, Liang Liu -- 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] REMD problem
Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -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] REMD problem
Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/**Documentation/How-tos/REMD#**Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- Best, Liang Liu -- 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] REMD problem
Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- ==__== 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 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin 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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 http://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- 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] REMD problem
Thanks for the information. I installed the mpi version with sudo apt-get install gromacs-openmpi under Ubuntu. Then run mdrun_mpi -s md.tpr -replex 10 -multi 10? Another error appears, The number of nodes (1) is not a multiple of the number of simulations (10). What is this for? On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/__**Documentation/How-tos/REMD#__** Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/**Documentation/How-tos/REMD#**Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- ==**__== 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 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://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-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- Best, Liang Liu -- 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] REMD problem
Liu, Liang wrote: Thanks for the information. I installed the mpi version with sudo apt-get install gromacs-openmpi under Ubuntu. Then run mdrun_mpi -s md.tpr -replex 10 -multi 10? Another error appears, The number of nodes (1) is not a multiple of the number of simulations (10). What is this for? You have to run mdrun_mpi as a process under mpirun, e.g.: mpirun -np 10 mdrun_mpi -s md.tpr (etc) -Justin On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- ==== 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 http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-request@__gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- ==__== 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 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin 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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface
Re: [gmx-users] REMD problem
This works. Thanks a lot. Currently I am running on an RNA molecule and I want to a 1 ns REMD simulations with 50 temperatures, would you please have a look at the following command mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50. Is this right? How to choose the numbers for np, multi or replex? Is the simulation time still set in the mdp file with nsteps and dt? e.g. nsteps = 50 and dt = 0.002 to run a 1ns simulation? Any helps will be highly appreciated. On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Thanks for the information. I installed the mpi version with sudo apt-get install gromacs-openmpi under Ubuntu. Then run mdrun_mpi -s md.tpr -replex 10 -multi 10? Another error appears, The number of nodes (1) is not a multiple of the number of simulations (10). What is this for? You have to run mdrun_mpi as a process under mpirun, e.g.: mpirun -np 10 mdrun_mpi -s md.tpr (etc) -Justin On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/** Documentation/How-tos/REMD#___**_Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__**Documentation/How-tos/REMD#__** Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/__** Documentation/How-tos/REMD#__**Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/**Documentation/How-tos/REMD#** Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- ==**== 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 http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org** http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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/Search http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www
Re: [gmx-users] REMD problem
Liu, Liang wrote: This works. Thanks a lot. Currently I am running on an RNA molecule and I want to a 1 ns REMD simulations with 50 temperatures, would you please have a look at the following command mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50. Is this right? How to choose the numbers for np, multi or replex? Current Gromacs versions allow more than one processor per REMD simulation. Please refer to the link I provided before for specifics. You need all of the replicas to run at roughly the same speed so the number of processors per simulation should be the same. Is the simulation time still set in the mdp file with nsteps and dt? e.g. nsteps = 50 and dt = 0.002 to run a 1ns simulation? It's just like any other simulation in this regard. -Justin Any helps will be highly appreciated. On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Thanks for the information. I installed the mpi version with sudo apt-get install gromacs-openmpi under Ubuntu. Then run mdrun_mpi -s md.tpr -replex 10 -multi 10? Another error appears, The number of nodes (1) is not a multiple of the number of simulations (10). What is this for? You have to run mdrun_mpi as a process under mpirun, e.g.: mpirun -np 10 mdrun_mpi -s md.tpr (etc) -Justin On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- ==__== 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 http://vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/__justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org
Re: [gmx-users] REMD problem
So if my personal computer have 2 cores, the np should be set to 2? Does it relate to -multi? How to choose a reasonable number for -replex? the smaller the better? Thanks again. On Wed, Sep 28, 2011 at 3:06 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: This works. Thanks a lot. Currently I am running on an RNA molecule and I want to a 1 ns REMD simulations with 50 temperatures, would you please have a look at the following command mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50. Is this right? How to choose the numbers for np, multi or replex? Current Gromacs versions allow more than one processor per REMD simulation. Please refer to the link I provided before for specifics. You need all of the replicas to run at roughly the same speed so the number of processors per simulation should be the same. Is the simulation time still set in the mdp file with nsteps and dt? e.g. nsteps = 50 and dt = 0.002 to run a 1ns simulation? It's just like any other simulation in this regard. -Justin Any helps will be highly appreciated. On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Liu, Liang wrote: Thanks for the information. I installed the mpi version with sudo apt-get install gromacs-openmpi under Ubuntu. Then run mdrun_mpi -s md.tpr -replex 10 -multi 10? Another error appears, The number of nodes (1) is not a multiple of the number of simulations (10). What is this for? You have to run mdrun_mpi as a process under mpirun, e.g.: mpirun -np 10 mdrun_mpi -s md.tpr (etc) -Justin On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/__** Documentation/How-tos/REMD#___**___Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/**Documentation/How-tos/REMD#___** _Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/** Documentation/How-tos/REMD#___**_Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__**Documentation/How-tos/REMD#__** Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/** Documentation/How-tos/REMD#___**_Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__**Documentation/How-tos/REMD#__** Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/__** Documentation/How-tos/REMD#__**Execution_Stepshttp://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/**Documentation/How-tos/REMD#** Execution_Stepshttp://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA
Re: [gmx-users] REMD problem
Liu, Liang wrote: So if my personal computer have 2 cores, the np should be set to 2? Does it relate to -multi? That means you can only run 2 replicates. Bad idea. You'll need access to a much better cluster to do anything meaningful. All REMD simulations have to be run simultaneously. If you want 50 replicas, you need at least 50 processors, ideally more. How to choose a reasonable number for -replex? the smaller the better? Please consult the literature. -Justin Thanks again. On Wed, Sep 28, 2011 at 3:06 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: This works. Thanks a lot. Currently I am running on an RNA molecule and I want to a 1 ns REMD simulations with 50 temperatures, would you please have a look at the following command mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50. Is this right? How to choose the numbers for np, multi or replex? Current Gromacs versions allow more than one processor per REMD simulation. Please refer to the link I provided before for specifics. You need all of the replicas to run at roughly the same speed so the number of processors per simulation should be the same. Is the simulation time still set in the mdp file with nsteps and dt? e.g. nsteps = 50 and dt = 0.002 to run a 1ns simulation? It's just like any other simulation in this regard. -Justin Any helps will be highly appreciated. On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Thanks for the information. I installed the mpi version with sudo apt-get install gromacs-openmpi under Ubuntu. Then run mdrun_mpi -s md.tpr -replex 10 -multi 10? Another error appears, The number of nodes (1) is not a multiple of the number of simulations (10). What is this for? You have to run mdrun_mpi as a process under mpirun, e.g.: mpirun -np 10 mdrun_mpi -s md.tpr (etc) -Justin On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Does that mean I have to use MPI? I got an error mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support after run mdrun -s md.tpr -multi 10 -replex 10 Per the error message, yes. -Justin On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as Need at least two replicas for replica exchange (option -multi), what is this for? Thanks. You have to use the -multi flag. Otherwise all mdrun does is run md.tpr and try to do REMD with nothing. http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps
Re: [gmx-users] REMD problem
Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. Thanks. -- Best, Liang Liu -- 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] REMD problem
Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- 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] REMD problem
Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- Best, Liang Liu -- 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] REMD problem
Liu, Liang wrote: Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? Are the log files being updated, or do they all simply contain a fatal error message that there are insufficient nodes? I cannot think of a reason why 50 simulations could possibly run on 2 processors. -Justin On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- ==__== 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 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin 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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 http://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- 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] REMD problem
Yes, they are updated like: ... Replica exchange at step 5700 time 11.4 Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 43 x 44 45 x 46 47 48 49 Repl pr1.0 1.0 1.0 .00 1.0 1.0 .00 1.0 1.0 1.0 1.0 .00 1.0 .00 1.0 .00 1.0 .00 .46 .00 1.0 .78 1.0 .00 Replica exchange at step 5750 time 11.5 Repl 0 - 1 dE = -7.583e+00 Repl ex 0 x 1234 x 56 x 78 x 9 10 x 11 12 x 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x 43 44 45 46 47 48 49 Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 .48 .11 1.0 .00 1.0 .00 1.0 .00 .00 .01 1.0 1.0 .00 .01 .01 Step Time Lambda 5800 11.60.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.69806e+021.32207e+033.34938e+014.93171e+02 -3.9e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+040.0e+00 PotentialKinetic En. Total Energy Conserved En.Temperature -1.78987e+054.57462e+04 -1.33240e+051.23302e+105.62201e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.12803e+02 -5.47109e+022.21484e-05 ... On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? Are the log files being updated, or do they all simply contain a fatal error message that there are insufficient nodes? I cannot think of a reason why 50 simulations could possibly run on 2 processors. -Justin On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- ==**__== 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 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://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-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Best, Liang Liu -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of
Re: [gmx-users] REMD problem
Liu, Liang wrote: Yes, they are updated like: ... Replica exchange at step 5700 time 11.4 Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 43 x 44 45 x 46 47 48 49 Repl pr1.0 1.0 1.0 .00 1.0 1.0 .00 1.0 1.0 1.0 1.0 .00 1.0 .00 1.0 .00 1.0 .00 .46 .00 1.0 .78 1.0 .00 Replica exchange at step 5750 time 11.5 Repl 0 - 1 dE = -7.583e+00 Repl ex 0 x 1234 x 56 x 78 x 9 10 x 11 12 x 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x 43 44 45 46 47 48 49 Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 .48 .11 1.0 .00 1.0 .00 1.0 .00 .00 .01 1.0 1.0 .00 .01 .01 Step Time Lambda 5800 11.60.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.69806e+021.32207e+033.34938e+014.93171e+02 -3.9e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+040.0e+00 PotentialKinetic En. Total Energy Conserved En.Temperature -1.78987e+054.57462e+04 -1.33240e+051.23302e+105.62201e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.12803e+02 -5.47109e+022.21484e-05 ... Perhaps someone else can offer an explanation. It should not be possible to run multiple replicas on a single processor. Also note that your exchange probability is extremely high; you're likely not obtaining meaningful sampling. -Justin On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? Are the log files being updated, or do they all simply contain a fatal error message that there are insufficient nodes? I cannot think of a reason why 50 simulations could possibly run on 2 processors. -Justin On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- ==== 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 http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please
[gmx-users] Fwd: pdb2gmx converting coordinates incorrectly.
-- Forwarded message -- From: William Welch wwelch...@gmail.com Date: Wed, Sep 28, 2011 at 3:43 PM Subject: pdb2gmx converting coordinates incorrectly. To: gmxus...@gromacs.org Friends, I generated a pdb for a tyrosineamide molecule and made an entry for it in ffcharmm27.rtp. Everything seems to be fucntional--I can make the .gro file and the .top file using pdb2gmx and subsequent processes seem to execute fine. The only problem is that when I look at the .gro file in VMD, I can see that the atoms have been moved to entirely different coordinates with respect to each other---I mean it's not even a real molecule, and certainly not the one I'm starting with Looking at the text of the .gro file, I see that the x cooridinate seems to have been converted correctly to nanometers, but the y and z coordinates are clearly wrong. Here are copies of the coordinates (the columns are aligned in the real files). This happens when I use pdb2gmx Version 4.0.5 PDB TITLE tyrosineamide2 REMARK 4 REMARK 4 COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996 REMARK 6 created by ArgusLab version 4.0.1 REMARK 6 http://www.arguslab.com REMARK 6 ATOM 1 NH3 TYRA ? 1 -1.797 5.686 -1.030 N ATOM 2 CA TYRA ? 1 -1.575 4.269 -0.716 C ATOM 3 CTYRA ? 1 -0.273 3.854 -1.311 C ATOM 4 OTYRA ? 1 0.570 3.201 -0.654 O ATOM 5 CB TYRA ? 1 -2.734 3.441 -1.274 C ATOM 6 CG TYRA ? 1 -3.924 3.374 -0.339 C ATOM 7 CD1 TYRA ? 1 -3.942 2.496 0.665 C ATOM 8 CD2 TYRA ? 1 -5.007 4.235 -0.538 C ATOM 9 CE1 TYRA ? 1 -5.072 2.449 1.563 C ATOM 10 CE2 TYRA ? 1 -6.152 4.156 0.320 C ATOM 11 CZ TYRA ? 1 -6.140 3.253 1.299 C ATOM 12 OH TYRA ? 1 -7.278 3.176 2.149 O ATOM 13 NH2 TYRA ? 1 0.019 4.207 -2.655 N ATOM 14 HA TYRA ? 1 -1.536 4.134 0.375 H ATOM 15 HB1 TYRA ? 1 -3.064 3.890 -2.223 H ATOM 16 HB2 TYRA ? 1 -2.380 2.416 -1.457 H ATOM 17 HD1 TYRA ? 1 -3.096 1.808 0.810 H ATOM 18 HD2 TYRA ? 1 -4.980 4.973 -1.354 H ATOM 19 HE1 TYRA ? 1 -5.055 1.776 2.433 H ATOM 20 HE2 TYRA ? 1 -7.007 4.829 0.160 H ATOM 21 HH TYRA ? 1 -7.154 2.339 2.852 H ATOM 22 HC1 TYRA ? 1 -0.899 6.265 -0.766 H ATOM 23 HC2 TYRA ? 1 -2.656 6.059 -0.453 H ATOM 24 HC3 TYRA ? 1 -2.000 5.796 -2.105 H ATOM 25 HN1 TYRA ? 1 0.976 3.907 -3.107 H ATOM 26 HN2 TYRA ? 1 -0.682 3.761 -3.376 H .gro tyrosineamide2 26 1TYRA NH31 -0.179 0.700 0.600 1TYRA HC12 -0.089 0.900 0.500 1TYRA HC23 -0.265 0.600 0.900 1TYRA HC34 -0.200 0.000 0.600 1TYRACA5 -0.157 0.500 0.900 1TYRAHA6 -0.153 0.600 0.400 1TYRACB7 -0.273 0.400 0.100 1TYRA HB18 -0.306 0.400 0.000 1TYRA HB29 -0.238 0.000 0.600 1TYRACG 10 -0.392 0.400 0.400 1TYRA CD1 11 -0.394 0.200 0.600 1TYRA HD1 12 -0.309 0.600 0.800 1TYRA CE1 13 -0.507 0.200 0.900 1TYRA HE1 14 -0.505 0.500 0.600 1TYRACZ 15 -0.614 0.000 0.300 1TYRAOH 16 -0.727 0.800 0.600 1TYRAHH 17 -0.715 0.400 0.900 1TYRA CD2 18 -0.500 0.700 0.500 1TYRA HD2 19 -0.498 0.000 0.300 1TYRA CE2 20 -0.615 0.200 0.600 1TYRA HE2 21 -0.700 0.700 0.900 1TYRA C 22 -0.027 0.300 0.400 1TYRA O 23 0.057 0.000 0.100 1TYRA NH2 24 0.001 0.900 0.700 1TYRA HN1 25 0.097 0.600 0.700 1TYRA HN2 26 -0.068 0.200 0.100 0.82400 0.9 0.9 Will -- 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] Fwd: pdb2gmx converting coordinates incorrectly.
William Welch wrote: -- Forwarded message -- From: *William Welch* wwelch...@gmail.com mailto:wwelch...@gmail.com Date: Wed, Sep 28, 2011 at 3:43 PM Subject: pdb2gmx converting coordinates incorrectly. To: gmxus...@gromacs.org mailto:gmxus...@gromacs.org Friends, I generated a pdb for a tyrosineamide molecule and made an entry for it in ffcharmm27.rtp. Everything seems to be fucntional--I can make the .gro file and the .top file using pdb2gmx and subsequent processes seem to execute fine. The only problem is that when I look at the .gro file in VMD, I can see that the atoms have been moved to entirely different coordinates with respect to each other---I mean it's not even a real molecule, and certainly not the one I'm starting with Looking at the text of the .gro file, I see that the x cooridinate seems to have been converted correctly to nanometers, but the y and z coordinates are clearly wrong. Here are copies of the coordinates (the columns are aligned in the real files). This happens when I use pdb2gmx Version 4.0.5 Your alignment is the problem. Compare the first line (from your file) with a standard PDB file: ATOM 1 NH3 TYRA ? 1 -1.797 5.686 -1.030 N ATOM 1 N LYS 1 35.360 22.340 -11.980 1.00 0.00 You can easily see that the coordinates are going to be junk. The PDB format requires fixed spacing. If this is not the case, you get unpredictable output. -Justin PDB TITLE tyrosineamide2 REMARK 4 REMARK 4 COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996 REMARK 6 created by ArgusLab version 4.0.1 REMARK 6 http://www.arguslab.com REMARK 6 ATOM 1 NH3 TYRA ? 1 -1.797 5.686 -1.030 N ATOM 2 CA TYRA ? 1 -1.575 4.269 -0.716 C ATOM 3 CTYRA ? 1 -0.273 3.854 -1.311 C ATOM 4 OTYRA ? 1 0.570 3.201 -0.654 O ATOM 5 CB TYRA ? 1 -2.734 3.441 -1.274 C ATOM 6 CG TYRA ? 1 -3.924 3.374 -0.339 C ATOM 7 CD1 TYRA ? 1 -3.942 2.496 0.665 C ATOM 8 CD2 TYRA ? 1 -5.007 4.235 -0.538 C ATOM 9 CE1 TYRA ? 1 -5.072 2.449 1.563 C ATOM 10 CE2 TYRA ? 1 -6.152 4.156 0.320 C ATOM 11 CZ TYRA ? 1 -6.140 3.253 1.299 C ATOM 12 OH TYRA ? 1 -7.278 3.176 2.149 O ATOM 13 NH2 TYRA ? 1 0.019 4.207 -2.655 N ATOM 14 HA TYRA ? 1 -1.536 4.134 0.375 H ATOM 15 HB1 TYRA ? 1 -3.064 3.890 -2.223 H ATOM 16 HB2 TYRA ? 1 -2.380 2.416 -1.457 H ATOM 17 HD1 TYRA ? 1 -3.096 1.808 0.810 H ATOM 18 HD2 TYRA ? 1 -4.980 4.973 -1.354 H ATOM 19 HE1 TYRA ? 1 -5.055 1.776 2.433 H ATOM 20 HE2 TYRA ? 1 -7.007 4.829 0.160 H ATOM 21 HH TYRA ? 1 -7.154 2.339 2.852 H ATOM 22 HC1 TYRA ? 1 -0.899 6.265 -0.766 H ATOM 23 HC2 TYRA ? 1 -2.656 6.059 -0.453 H ATOM 24 HC3 TYRA ? 1 -2.000 5.796 -2.105 H ATOM 25 HN1 TYRA ? 1 0.976 3.907 -3.107 H ATOM 26 HN2 TYRA ? 1 -0.682 3.761 -3.376 H .gro tyrosineamide2 26 1TYRA NH31 -0.179 0.700 0.600 1TYRA HC12 -0.089 0.900 0.500 1TYRA HC23 -0.265 0.600 0.900 1TYRA HC34 -0.200 0.000 0.600 1TYRACA5 -0.157 0.500 0.900 1TYRAHA6 -0.153 0.600 0.400 1TYRACB7 -0.273 0.400 0.100 1TYRA HB18 -0.306 0.400 0.000 1TYRA HB29 -0.238 0.000 0.600 1TYRACG 10 -0.392 0.400 0.400 1TYRA CD1 11 -0.394 0.200 0.600 1TYRA HD1 12 -0.309 0.600 0.800 1TYRA CE1 13 -0.507 0.200 0.900 1TYRA HE1 14 -0.505 0.500 0.600 1TYRACZ 15 -0.614 0.000 0.300 1TYRAOH 16 -0.727 0.800 0.600 1TYRAHH 17 -0.715 0.400 0.900 1TYRA CD2 18 -0.500 0.700 0.500 1TYRA HD2 19 -0.498 0.000 0.300 1TYRA CE2 20 -0.615 0.200 0.600 1TYRA HE2 21 -0.700 0.700 0.900 1TYRA C 22 -0.027 0.300 0.400 1TYRA O 23 0.057 0.000 0.100 1TYRA NH2 24 0.001 0.900 0.700 1TYRA HN1 25 0.097 0.600 0.700 1TYRA HN2 26
Re: [gmx-users] REMD problem
On 29/09/2011 7:20 AM, Justin A. Lemkul wrote: Liu, Liang wrote: Yes, they are updated like: ... Replica exchange at step 5700 time 11.4 Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 43 x 44 45 x 46 47 48 49 Repl pr1.0 1.0 1.0 .00 1.0 1.0 .00 1.0 1.0 1.0 1.0 .00 1.0 .00 1.0 .00 1.0 .00 .46 .00 1.0 .78 1.0 .00 Replica exchange at step 5750 time 11.5 Repl 0 - 1 dE = -7.583e+00 Repl ex 0 x 1234 x 56 x 78 x 9 10 x 11 12 x 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x 43 44 45 46 47 48 49 Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 .48 .11 1.0 .00 1.0 .00 1.0 .00 .00 .01 1.0 1.0 .00 .01 .01 Step Time Lambda 5800 11.60.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.69806e+021.32207e+033.34938e+014.93171e+02 -3.9e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+04 0.0e+00 PotentialKinetic En. Total Energy Conserved En. Temperature -1.78987e+054.57462e+04 -1.33240e+051.23302e+10 5.62201e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.12803e+02 -5.47109e+022.21484e-05 ... Perhaps someone else can offer an explanation. It should not be possible to run multiple replicas on a single processor. Also note that your exchange probability is extremely high; you're likely not obtaining meaningful sampling. If the MPI configuration allows physical processors to be over-allocated, then GROMACS is none the wiser. Mark -Justin On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? Are the log files being updated, or do they all simply contain a fatal error message that there are insufficient nodes? I cannot think of a reason why 50 simulations could possibly run on 2 processors. -Justin On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- ==== 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 http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/__mailman/listinfo/gmx-users
Re: [gmx-users] REMD problem
Not know. I will update the result tomorrow, as the 5 steps take really long time :( On Wed, Sep 28, 2011 at 4:38 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/09/2011 7:20 AM, Justin A. Lemkul wrote: Liu, Liang wrote: Yes, they are updated like: ... Replica exchange at step 5700 time 11.4 Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 43 x 44 45 x 46 47 48 49 Repl pr1.0 1.0 1.0 .00 1.0 1.0 .00 1.0 1.0 1.0 1.0 .00 1.0 .00 1.0 .00 1.0 .00 .46 .00 1.0 .78 1.0 .00 Replica exchange at step 5750 time 11.5 Repl 0 - 1 dE = -7.583e+00 Repl ex 0 x 1234 x 56 x 78 x 9 10 x 11 12 x 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x 43 44 45 46 47 48 49 Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 .48 .11 1.0 .00 1.0 .00 1.0 .00 .00 .01 1.0 1.0 .00 .01 .01 Step Time Lambda 5800 11.60.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.69806e+021.32207e+033.34938e+014.93171e+02 -3.9e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+04 0.0e+00 PotentialKinetic En. Total Energy Conserved En. Temperature -1.78987e+054.57462e+04 -1.33240e+051.23302e+10 5.62201e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.12803e+02 -5.47109e+022.21484e-05 ... Perhaps someone else can offer an explanation. It should not be possible to run multiple replicas on a single processor. Also note that your exchange probability is extremely high; you're likely not obtaining meaningful sampling. If the MPI configuration allows physical processors to be over-allocated, then GROMACS is none the wiser. Mark -Justin On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Liu, Liang wrote: Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? Are the log files being updated, or do they all simply contain a fatal error message that there are insufficient nodes? I cannot think of a reason why 50 simulations could possibly run on 2 processors. -Justin On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Well, although this makes sense, why all the 50 replicas are running when I run mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50 on my own computer with only 2 cores? I can offer no explanation for this behavior, but I expect that either not all of them are actually running, or at the very least you will get horribly slow performance. By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. A few minutes of real literature searching will be far more valuable than some random person on the Internet giving you a value that you blindly use ;) -Justin Thanks. -- Best, Liang Liu -- ==**== 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 http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] Re: simulation of protein/water and phosphate ion
I repeated the nvt equilibration with 500 ps and it was successful , after confirming the temperature graph. But during npt simulation, I got the following error:- step 131500, will finish Thu Sep 29 01:54:20 2011imb F 2% step 131520: Water molecule starting at atom 6981 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.5.4 Source code file: pme.c, line: 538 Fatal error: 1 particles communicated to PME node 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. Since there are large no. of water molecules after 6981 , it means that it is not happening because oh some interaction with phosphate ion. What shall be done to rectify this ?? On Wed, Sep 28, 2011 at 12:35 PM, Dallas Warren dallas.war...@monash.eduwrote: And where are these waters? Close to the phosphate ions? ** ** You really need to be asking more questions, looking at the trajectory file / frames when it blows up, and determining what is actually going on by yourself. ** ** Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. ** ** *From:* gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] *On Behalf Of *bharat gupta *Sent:* Wednesday, 28 September 2011 1:30 PM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] Re: simulation of protein/water and phosphate ion** ** ** ** it's showing error that certain atoms cannot be settled and these atoms are of solvent molecules i.e. Water On Wednesday, September 28, 2011, Dallas Warren dallas.war...@monash.edu wrote: What is actually blowing up? The protein or the phosphate ions? Do the phosphate ions run OK by themselves in water? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] On Behalf Of bharat gupta Sent: Wednesday, 28 September 2011 12:48 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Re: simulation of protein/water and phosphate ion Hi, I tried simulating the system again but this time with 2 phsophate ion and the charge of the system was neutralized by adding 6 sodium ions . After minimizing , I equilibrated for 500 ps but I got LINCS error around 300ps. It's happening due to the addition of phosphate ions as I have simulated my protein in water earlier without any problem. During nvt quilibration the temperature coupling settings were for Protein and Non protein groups. Do I have to make groups for Protein and water_ion. Please comment?? On Tue, Sep 27, 2011 at 7:09 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: HI, I have tried simulating my protein (GFP) solvated with water molecules and 10 phosphate ions. During the md run step the system starts exploding after 500 ps. What could be the reason for this . I know this is happening due to the addition of phosphate ion but I need to study the binding of ions . So, what shall I do ?? http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -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 -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. -
Re: [gmx-users] Re: simulation of protein/water and phosphate ion
On 29/09/2011 9:59 AM, bharat gupta wrote: I repeated the nvt equilibration with 500 ps and it was successful , after confirming the temperature graph. But during npt simulation, I got the following error:- You are rearranging the deck chairs on a ship that is already sinking. You've been given good advice from several people - see http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System. There's nothing more to be said if you don't go and follow the advice there. You've got a complex piece of machinery that isn't working for unknown reasons. Diagnosing what is wrong is hard, but only you have the information, motivation and resources to do it. step 131500, will finish Thu Sep 29 01:54:20 2011imb F 2% step 131520: Water molecule starting at atom 6981 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.5.4 Source code file: pme.c, line: 538 Fatal error: 1 particles communicated to PME node 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. Since there are large no. of water molecules after 6981 , it means that it is not happening because oh some interaction with phosphate ion. There is no correlation between atom number and geometric proximity to a suspect molecule. You have to go and look at the initial structure and the trajectory. Mark What shall be done to rectify this ?? On Wed, Sep 28, 2011 at 12:35 PM, Dallas Warren dallas.war...@monash.edu mailto:dallas.war...@monash.edu wrote: And where are these waters? Close to the phosphate ions? You really need to be asking more questions, looking at the trajectory file / frames when it blows up, and determining what is actually going on by yourself. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu mailto:dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:*gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *bharat gupta *Sent:* Wednesday, 28 September 2011 1:30 PM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] Re: simulation of protein/water and phosphate ion it's showing error that certain atoms cannot be settled and these atoms are of solvent molecules i.e. Water On Wednesday, September 28, 2011, Dallas Warren dallas.war...@monash.edu mailto:dallas.war...@monash.edu wrote: What is actually blowing up? The protein or the phosphate ions? Do the phosphate ions run OK by themselves in water? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu mailto:dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] On Behalf Of bharat gupta Sent: Wednesday, 28 September 2011 12:48 PM To: jalem...@vt.edu mailto:jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Re: simulation of protein/water and phosphate ion Hi, I tried simulating the system again but this time with 2 phsophate ion and the charge of the system was neutralized by adding 6 sodium ions . After minimizing , I equilibrated for 500 ps but I got LINCS error around 300ps. It's happening due to the addition of phosphate ions as I have simulated my protein in water earlier without any problem. During nvt quilibration the temperature coupling settings were for Protein and Non protein groups. Do I have to make groups for Protein and water_ion. Please comment?? On Tue, Sep 27, 2011 at 7:09 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: HI, I have tried simulating my protein (GFP) solvated with water molecules and 10 phosphate ions. During the md run step the system starts exploding after 500 ps. What could be the reason for this . I know this is happening due to the addition
[gmx-users] Runs OK on small CPS but fails on large number of CPUs...
Dear Co-users, I have a systems made of simple molecules, KNO3 to say. A classical MD runs to completion on a supercomputer when using 24 CPUs only and fails after few hundreds of ps, not always at the same step, when I increase the number of CPUs to 72, 84, 96 ... The error message is as follows: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. I do know for facts that the system is very well equilibrated since the system had previously been equilibrated with EM on another machine until the energy does not change any more. Is there any brilliant idea out there? Thanks in advance for your help. Regards, Adama __ Dr. Adama Tandia | Modeling Simulation, Corning INC, Corning, NY 14831 USA | Tel: (+1) 607 248 1036 -- 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] Runs OK on small CPS but fails on large number of CPUs...
On 29/09/2011 12:44 PM, Tandia, Adama wrote: Dear Co-users, I have a systems made of simple molecules, KNO3 to say. A classical MD runs to completion on a supercomputer when using 24 CPUs only and fails after few hundreds of ps, not always at the same step, when I increase the number of CPUs to 72, 84, 96 ... The error message is as follows: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. A given simulation system and code cannot scale efficiently to an arbitrary number of processors. GROMACS needs about 500-1000 atoms per processor to get good value. Close to the lower limit, things become increasingly likely to break. However, it is likely that your system is not actually equilibrated. I do know for facts that the system is very well equilibrated since the system had previously been equilibrated with EM on another machine until the energy does not change any more. Successful EM does not imply equilibration, or nobody would ever worry about equilibration once EM succeeded... Mark Is there any brilliant idea out there? Thanks in advance for your help. Regards, Adama __ Dr. Adama Tandia | Modeling Simulation, Corning INC, Corning, NY 14831 USA | Tel: (+1) 607 248 1036 -- 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
