[gmx-users] total charge of the system
Hi, In my simulation, total charge of the system is a noninteger number (System has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine atoms. Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr Fatal error: moleculetype CU1 is redefined is it some thing wrong? Below is the first and final version of the .top file: First topol.top File ** [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL127 SOL157 SOL 41779 ** Final topol.top File *#include ions.itp* [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL127 SOL157 SOL *41771* *CL- 8* -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] total charge of the system
On 01/25/11, ahmet yıldırım ahmedo...@gmail.com wrote: Hi, In my simulation, total charge of the system is a noninteger number (System has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine atoms. Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr Fatal error: moleculetype CU1 is redefined is it some thing wrong? ions.itp defines molecule types for ions. Molecule types cannot be redefined. When you #included ions.itp GROMACS thought you were doing illegal redefinitions. Look back in the .top to find the original definitions, and then take suitable action. Mark Below is the first and final version of the .top file: First topol.top File [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 41779 Final topol.top File #include ions.itp [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 41771 CL- 8 -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] total charge of the system
Dear Mark, I looked at gromacs mail list but I could not find a proper solution .Whatshould I add to the .top file? Please look at the following reconstructed1 .top and reconstructed1 .top files I have error as the following reconstructed1 .top file: *Fatal error:* moleculetype CU1 is redefined I have error as the following reconstructed2 .top file: *Fatal error:* No such moleculetype CL- * Original .top file:* ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL10 SOL 127 SOL 157 SOL 41779 *reconstructed1 .top file* ; Include topology for ions #include gromos43a1.ff/ions.itp *#include ions.itp* [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL10 SOL 127 SOL 157 SOL 4177*1* CL- *8* *reconstructed2 .top file* ; Include topology for ions #include gromos43a1.ff/ions.itp ** [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL10 SOL 127 SOL 157 SOL 4177*1* CL- *8* 25 Ocak 2011 10:49 tarihinde Mark Abraham mark.abra...@anu.edu.au yazdı: On 01/25/11, *ahmet yıldırım * ahmedo...@gmail.com wrote: Hi, In my simulation, total charge of the system is a noninteger number (System has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine atoms. Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr Fatal error: moleculetype CU1 is redefined is it some thing wrong? ions.itp defines molecule types for ions. Molecule types cannot be redefined. When you #included ions.itp GROMACS thought you were doing illegal redefinitions. Look back in the .top to find the original definitions, and then take suitable action. Mark Below is the first and final version of the .top file: First topol.top File ** [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL127 SOL157 SOL 41779 ** Final topol.top File *#include ions.itp* [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL127 SOL157 SOL *41771* *CL- 8* -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] total charge of the system
On 01/25/11, ahmet yıldırım ahmedo...@gmail.com wrote: Dear Mark, I looked at gromacs mail list but I could not find a proper solution .What should I add to the .top file? Please look at the following reconstructed1 .top and reconstructed1 .top files I have error as the following reconstructed1 .top file: Fatal error: moleculetype CU1 is redefined I have error as the following reconstructed2 .top file: Fatal error: No such moleculetype CL- I don't have any knowledge of the context, so can't answer. It looks to me like you are mixing copies of ions.itp from multiple sources. Don't. Use the one for the force field you are targetting. pdb2gmx generated the right invocation - all you should have to do is use that by generating correctly-named ions. See http://www.gromacs.org/Documentation/Gromacs_Utilities/genion(http://www.gromacs.org/Documentation/Gromacs_Utilities/genion) Mark Original .top file: ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 41779 reconstructed1 .top file ; Include topology for ions #include gromos43a1.ff/ions.itp #include ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 41771 CL- 8 reconstructed2 .top file ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 41771 CL- 8 25 Ocak 2011 10:49 tarihinde Mark Abraham mark.abra...@anu.edu.au yazdı: On 01/25/11, ahmet yıldırım ahmedo...@gmail.com wrote: Hi, In my simulation, total charge of the system is a noninteger number (System has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine atoms. Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr Fatal error: moleculetype CU1 is redefined is it some thing wrong? ions.itp defines molecule types for ions. Molecule types cannot be redefined. When you #included ions.itp GROMACS thought you were doing illegal redefinitions. Look back in the .top to find the original definitions, and then take suitable action. Mark Below is the first and final version of the .top file: First topol.top File [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 41779 Final topol.top File #include ions.itp [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 41771 CL- 8 -- Ahmet YILDIRIM -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Secondary structure loss in implicit solvent simulations
Hi It's not necessarily GPU-specific, it's implicit solvent-specific. I don't get these problems in explicit solvent simulations on CPU, only in implicit solvent simulations both on GPU as well as CPU. One of the problems that I can think of is unbalanced charges that I would have balanced out using NaCl ions, but not any more. Regards Kush -- Kushagra Singhal Promovendus, Computational Chemistry van 't Hoff Institute of Molecular Sciences Science Park 904, room C2.119 1098 XH Amsterdam, The Netherlands +31 205256965 Universiteit van Amsterdam k.sing...@uva.nl -- 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
Antw: Re: [gmx-users] total charge of the system
Hello, You have to look into your ions.itp which is included in your top-file by #include ions.itp. There all the types of ions have to be defined. The atom-types which you can see in the ions.itp, you will find in the ffyour-forcefield.itp where your atomtypes are defined. On top of your .top file the Atomtype-itp-file is included. All these files are normally placed in /usr/share/gromacs/top/. But you also can place them into your current directory. Bests, Emanuel Mark Abraham 25.01.11 10.48 Uhr On 01/25/11, ahmet yıldırım wrote:Dear Mark, I looked at gromacs mail list but I could not find a proper solution .What should I add to the .top file? Please look at the following reconstructed1 .top and reconstructed1 .top files I have error as the following reconstructed1 .top file: Fatal error: moleculetype CU1 is redefined I have error as the following reconstructed2 .top file: Fatal error: No such moleculetype CL- I don't have any knowledge of the context, so can't answer. It looks to me like you are mixing copies of ions.itp from multiple sources. Don't. Use the one for the force field you are targetting. pdb2gmx generated the right invocation - all you should have to do is use that by generating correctly-named ions. See http://www.gromacs.org/Documentation/Gromacs_Utilities/genion Mark Original .top file: ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL10 SOL 127 SOL 157 SOL 41779 reconstructed1 .top file ; Include topology for ions #include gromos43a1.ff/ions.itp #include ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL10 SOL 127 SOL 157 SOL 41771 CL- 8 reconstructed2 .top file ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL10 SOL 127 SOL 157 SOL 41771 CL- 8 25 Ocak 2011 10:49 tarihinde Mark Abraham mark.abra...@anu.edu.au yazdı: On 01/25/11, ahmet yıldırım ahmedo...@gmail.com wrote:Hi, In my simulation, total charge of the system is a noninteger number (System has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine atoms. Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr Fatal error: moleculetype CU1 is redefined is it some thing wrong? ions.itp defines molecule types for ions. Molecule types cannot be redefined. When you #included ions.itp GROMACS thought you were doing illegal redefinitions. Look back in the .top to find the original definitions, and then take suitable action. Mark Below is the first and final version of the .top file: First topol.top File [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL127 SOL157 SOL 41779 Final topol.top File #include ions.itp [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL127 SOL157 SOL 41771 CL- 8 -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Re: [gmx-users] total charge of the system
Dear Mark and Emanuel, I am sending the ions.tip and the topol.top files. Everything seems ok. Any problem about these files? By the way, I am using the Gromacs 4.5.3. Force Field 43a1 25 Ocak 2011 12:03 tarihinde Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de yazdı: Hello, You have to look into your ions.itp which is included in your top-file by #include ions.itp. There all the types of ions have to be defined. The atom-types which you can see in the ions.itp, you will find in the ffyour-forcefield.itp where your atomtypes are defined. On top of your .top file the Atomtype-itp-file is included. All these files are normally placed in /usr/share/gromacs/top/. But you also can place them into your current directory. Bests, Emanuel Mark Abraham 25.01.11 10.48 Uhr On 01/25/11, *ahmet yıldırım * ahmedo...@gmail.com wrote: Dear Mark, I looked at gromacs mail list but I could not find a proper solution .Whatshould I add to the .top file? Please look at the following reconstructed1 .top and reconstructed1 .top files I have error as the following reconstructed1 .top file: *Fatal error:* moleculetype CU1 is redefined I have error as the following reconstructed2 .top file: *Fatal error:* No such moleculetype CL- ** I don't have any knowledge of the context, so can't answer. It looks to me like you are mixing copies of ions.itp from multiple sources. Don't. Use the one for the force field you are targetting. pdb2gmx generated the right invocation - all you should have to do is use that by generating correctly-named ions. Seehttp://www.gromacs.org/Documentation/Gromacs_Utilities/genion Mark *Original .top file:* ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL10 SOL 127 SOL 157 SOL 41779 *reconstructed1 .top file* ; Include topology for ions #include gromos43a1.ff/ions.itp *#include ions.itp* [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL10 SOL 127 SOL 157 SOL 4177*1* CL- *8* *reconstructed2 .top file* ; Include topology for ions #include gromos43a1.ff/ions.itp ** [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL10 SOL 127 SOL 157 SOL 4177*1* CL- *8* 25 Ocak 2011 10:49 tarihinde Mark Abraham mark.abra...@anu.edu.au yazdı: On 01/25/11, *ahmet yıldırım * ahmedo...@gmail.com wrote: Hi, In my simulation, total charge of the system is a noninteger number (System has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine atoms. Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr Fatal error: moleculetype CU1 is redefined is it some thing wrong? ions.itp defines molecule types for ions. Molecule types cannot be redefined. When you #included ions.itp GROMACS thought you were doing illegal redefinitions. Look back in the .top to find the original definitions, and then take suitable action. Mark Below is the first and final version of the .top file: First topol.top File ** [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL127 SOL157 SOL 41779 ** Final topol.top File *#include ions.itp* [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL127 SOL157 SOL *41771* *CL- 8* -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't
Re: Re: [gmx-users] total charge of the system
On 01/25/11, ahmet yıldırım ahmedo...@gmail.com wrote: Dear Mark and Emanuel, I am sending the ions.tip and the topol.top files. Everything seems ok. Any problem about these files? No. So one of the other #include files is erroneously defining ion molecule types. See www.gromacs.org/Documentation/Include_File_Mechanism. Go and read them and fix it. As the link I sent last time hinted, you need to name *molecules* in the [molecules] directive. Look carefully at the *molecule* name of chloride where it is defined. Mark By the way, I am using the Gromacs 4.5.3. Force Field 43a1 25 Ocak 2011 12:03 tarihinde Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de yazdı: Hello, You have to look into your ions.itp which is included in your top-file by #include ions.itp. There all the types of ions have to be defined. The atom-types which you can see in the ions.itp, you will find in the ffyour-forcefield.itp where your atomtypes are defined. On top of your .top file the Atomtype-itp-file is included. All these files are normally placed in /usr/share/gromacs/top/. But you also can place them into your current directory. Bests, Emanuel Mark Abraham 25.01.11 10.48 Uhr On 01/25/11, ahmet yıldırım ahmedo...@gmail.com wrote: Dear Mark, I looked at gromacs mail list but I could not find a proper solution .What should I add to the .top file? Please look at the following reconstructed1 .top and reconstructed1 .top files I have error as the following reconstructed1 .top file: Fatal error: moleculetype CU1 is redefined I have error as the following reconstructed2 .top file: Fatal error: No such moleculetype CL- I don't have any knowledge of the context, so can't answer. It looks to me like you are mixing copies of ions.itp from multiple sources. Don't. Use the one for the force field you are targetting. pdb2gmx generated the right invocation - all you should have to do is use that by generating correctly-named ions. See http://www.gromacs.org/Documentation/Gromacs_Utilities/genion(http://www.gromacs.org/Documentation/Gromacs_Utilities/genion) Mark Original .top file: ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 41779 reconstructed1 .top file ; Include topology for ions #include gromos43a1.ff/ions.itp #include ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 41771 CL- 8 reconstructed2 .top file ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 41771 CL- 8 25 Ocak 2011 10:49 tarihinde Mark Abraham mark.abra...@anu.edu.au yazdı: On 01/25/11, ahmet yıldırım ahmedo...@gmail.com wrote: Hi, In my simulation, total charge of the system is a noninteger number (System has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine atoms. Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr Fatal error: moleculetype CU1 is redefined is it some thing wrong? ions.itp defines molecule types for ions. Molecule types cannot be redefined. When you #included ions.itp GROMACS thought you were doing illegal redefinitions. Look back in the .top to find the original definitions, and then take suitable action. Mark Below is the first and final version of the .top file: First topol.top File [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127
Re: Re: [gmx-users] total charge of the system
Dear Mark, A million thanks. Problem is solved. Finally, Select a continuous group of solvent molecules: ... Group12 ( Water) has 126219 elements Group13 (SOL) has 126219 elements Which one should I choose 12 or 13? *Final topol.top file: *;File 'topol.top' was generated ;By user: onbekend (0) ;On host: onbekend ;At date: Tue Jan 25 10:12:14 2011 ; ;This is a standalone topology file ; ;It was generated using program: ;pdb2gmx - VERSION 4.5.3 ; ;Command line was: ;pdb2gmx -f 3MOA.pdb -water spc -ter ; ;Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include gromos43a1.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_P.itp #include topol_Protein_chain_L.itp #include topol_Protein_chain_H.itp ; Include water topology #include gromos43a1.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL10 SOL 127 SOL 157 SOL 41771 *CL 8 * 25 Ocak 2011 13:13 tarihinde Mark Abraham mark.abra...@anu.edu.au yazdı: On 01/25/11, *ahmet yıldırım * ahmedo...@gmail.com wrote: Dear Mark and Emanuel, I am sending the ions.tip and the topol.top files. Everything seems ok. Any problem about these files? No. So one of the other #include files is erroneously defining ion molecule types. See www.gromacs.org/Documentation/Include_File_Mechanism. Go and read them and fix it. As the link I sent last time hinted, you need to name *molecules* in the [molecules] directive. Look carefully at the *molecule* name of chloride where it is defined. Mark By the way, I am using the Gromacs 4.5.3. Force Field 43a1 25 Ocak 2011 12:03 tarihinde Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de yazdı: Hello, You have to look into your ions.itp which is included in your top-file by #include ions.itp. There all the types of ions have to be defined. The atom-types which you can see in the ions.itp, you will find in the ffyour-forcefield.itp where your atomtypes are defined. On top of your .top file the Atomtype-itp-file is included. All these files are normally placed in /usr/share/gromacs/top/. But you also can place them into your current directory. Bests, Emanuel Mark Abraham 25.01.11 10.48 Uhr On 01/25/11, *ahmet yıldırım * ahmedo...@gmail.com wrote: Dear Mark, I looked at gromacs mail list but I could not find a proper solution . What should I add to the .top file? Please look at the following reconstructed1 .top and reconstructed1 .top files I have error as the following reconstructed1 .top file: *Fatal error:* moleculetype CU1 is redefined I have error as the following reconstructed2 .top file: *Fatal error:* No such moleculetype CL- ** I don't have any knowledge of the context, so can't answer. It looks to me like you are mixing copies of ions.itp from multiple sources. Don't. Use the one for the force field you are targetting. pdb2gmx generated the right invocation - all you should have to do is use that by generating correctly-named ions. Seehttp://www.gromacs.org/Documentation/Gromacs_Utilities/genion Mark *Original .top file:* ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL10 SOL 127 SOL 157 SOL 41779 *reconstructed1 .top file* ; Include topology for ions #include gromos43a1.ff/ions.itp *#include ions.itp* [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL10 SOL 127 SOL 157 SOL 4177*1* CL- *8* *reconstructed2 .top file* ; Include topology for ions #include gromos43a1.ff/ions.itp ** [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound#mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL10 SOL 127 SOL 157 SOL 4177*1* CL-
Re: Re: [gmx-users] total charge of the system
On 01/25/11, ahmet yıldırım ahmedo...@gmail.com wrote: Dear Mark, A million thanks. Problem is solved. Finally, Select a continuous group of solvent molecules: ... Group 12 ( Water) has 126219 elements Group 13 ( SOL) has 126219 elements Which one should I choose 12 or 13? They're probably the same. Mark Final topol.top file: ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue Jan 25 10:12:14 2011 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.3 ; ; Command line was: ; pdb2gmx -f 3MOA.pdb -water spc -ter ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include gromos43a1.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_P.itp #include topol_Protein_chain_L.itp #include topol_Protein_chain_H.itp ; Include water topology #include gromos43a1.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 41771 CL 8 25 Ocak 2011 13:13 tarihinde Mark Abraham mark.abra...@anu.edu.au yazdı: On 01/25/11, ahmet yıldırım ahmedo...@gmail.com wrote: Dear Mark and Emanuel, I am sending the ions.tip and the topol.top files. Everything seems ok. Any problem about these files? No. So one of the other #include files is erroneously defining ion molecule types. See www.gromacs.org/Documentation/Include_File_Mechanism(http://www.gromacs.org/Documentation/Include_File_Mechanism). Go and read them and fix it. As the link I sent last time hinted, you need to name *molecules* in the [molecules] directive. Look carefully at the *molecule* name of chloride where it is defined. Mark By the way, I am using the Gromacs 4.5.3. Force Field 43a1 25 Ocak 2011 12:03 tarihinde Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de yazdı: Hello, You have to look into your ions.itp which is included in your top-file by #include ions.itp. There all the types of ions have to be defined. The atom-types which you can see in the ions.itp, you will find in the ffyour-forcefield.itp where your atomtypes are defined. On top of your .top file the Atomtype-itp-file is included. All these files are normally placed in /usr/share/gromacs/top/. But you also can place them into your current directory. Bests, Emanuel Mark Abraham 25.01.11 10.48 Uhr On 01/25/11, ahmet yıldırım ahmedo...@gmail.com wrote: Dear Mark, I looked at gromacs mail list but I could not find a proper solution .What should I add to the .top file? Please look at the following reconstructed1 .top and reconstructed1 .top files I have error as the following reconstructed1 .top file: Fatal error: moleculetype CU1 is redefined I have error as the following reconstructed2 .top file: Fatal error: No such moleculetype CL- I don't have any knowledge of the context, so can't answer. It looks to me like you are mixing copies of ions.itp from multiple sources. Don't. Use the one for the force field you are targetting. pdb2gmx generated the right invocation - all you should have to do is use that by generating correctly-named ions. See http://www.gromacs.org/Documentation/Gromacs_Utilities/genion(http://www.gromacs.org/Documentation/Gromacs_Utilities/genion) Mark Original .top file: ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 41779 reconstructed1 .top file ; Include topology for ions #include gromos43a1.ff/ions.itp #include ions.itp
[gmx-users] Can not open file: run.xtc
Dear users, g_rms -s em.tpr -f run.xtc Select group for least squares fit: Selected 2: 'Protein-H' Select group for RMSD calculation Selected 2: 'Protein-H' I didn't had such a problem in other samples. But now, I have the error as the following: Program g_rms, VERSION 4.5.3 Source code file: gmxfio.c, line: 519 Can not open file: run.xtc -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97
HI Friends, I get the following note, The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. I want to keep the T at 300K, so does it matter to select any thermostat method? Another note when i use PME: Estimate for the relative computational load of the PME mesh part: 0.97 NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing So what is the reason? I use type=PME Is my setting proper? 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] Can not open file: run.xtc
Hi Ahmet, That sort of indicates that the file is not there, doesn't it? Maybe you're not doing what you expect to be doing, or doing it somewhere else. Cheers, Tsjerk 2011/1/25 ahmet yıldırım ahmedo...@gmail.com: Dear users, g_rms -s em.tpr -f run.xtc Select group for least squares fit: Selected 2: 'Protein-H' Select group for RMSD calculation Selected 2: 'Protein-H' I didn't had such a problem in other samples. But now, I have the error as the following: Program g_rms, VERSION 4.5.3 Source code file: gmxfio.c, line: 519 Can not open file: run.xtc -- Ahmet YILDIRIM -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97
gromacs wrote: HI Friends, I get the following note, The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. I want to keep the T at 300K, so does it matter to select any thermostat method? The choice of thermostat certainly does matter, otherwise you wouldn't get this note. Refer to the numerous discussions in the list archive as to why one would or would not (usually) use the Berendsen thermostat, as well as: http://www.gromacs.org/Documentation/Terminology/Thermostats http://www.gromacs.org/Documentation/Terminology/Berendsen Another note when i use PME: Estimate for the relative computational load of the PME mesh part: 0.97 NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing So what is the reason? I use type=PME Your combination of settings (rcoulomb, fourierspacing, and perhaps a few others) indicate that your simulation is going to spend an inordinate amount of time doing PME calculations, so your performance will suffer. Seeing your entire .mdp file would be necessary if you want further guidance. -Justin Is my setting proper? Thanks -- 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] Can not open file: run.xtc
Dear Tsjerk, Thank you. Problem solved. g_rms -s em.tpr -f run.trr -o rmsd.xvg xmgrace rmsd.xvg 25 Ocak 2011 14:51 tarihinde Tsjerk Wassenaar tsje...@gmail.com yazdı: Hi Ahmet, That sort of indicates that the file is not there, doesn't it? Maybe you're not doing what you expect to be doing, or doing it somewhere else. Cheers, Tsjerk 2011/1/25 ahmet yıldırım ahmedo...@gmail.com: Dear users, g_rms -s em.tpr -f run.xtc Select group for least squares fit: Selected 2: 'Protein-H' Select group for RMSD calculation Selected 2: 'Protein-H' I didn't had such a problem in other samples. But now, I have the error as the following: Program g_rms, VERSION 4.5.3 Source code file: gmxfio.c, line: 519 Can not open file: run.xtc -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] compiling error in tools
Hello I know this is possibly an issue for the IT support at my Uni but I was wondering if someone could shed some light on what may have gone wrong so at least I can point them in the right direction. As I am getting very small diffusion coefficients when using g_msd, I want to increase the number of decimal points the diffusion coefficient is displayed to. In the file gmx_msd.c within src/tools I changed fprintf(out,# D[%10s] = %.4f (+/- %.4f) (1e-5 cm^2/s)\n, to fprintf(out,# D[%10s] = %.8f (+/- %.8f) (1e-5 cm^2/s)\n, then, as I have always done, I just typed in make g_msd to recompile this tool. I get the following error message: src/tools make g_msd mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\/home/jwillia4/GRO/share/top\ -I/home/jwillia4/GRO/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT g_msd.o -MD -MP -MF .deps/g_msd.Tpo -c -o g_msd.o g_msd.c mv -f .deps/g_msd.Tpo .deps/g_msd.Po /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/home/jwillia4/GRO/lib -lgslcblas -o g_msd g_msd.o libgmxana_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la -lgsl -lnsl -lfftw3f -lm mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o g_msd g_msd.o -L/home/jwillia4/GRO/lib ./.libs/libgmxana_mpi.a /home/jwillia4/GRO/gromacs-4.0.7/src/mdlib/.libs/libmd_mpi.a ../mdlib/.libs/libmd_mpi.a /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a ../gmxlib/.libs/libgmx_mpi.a /home/jwillia4/GRO/lib/libgslcblas.so /home/jwillia4/GRO/lib/libgsl.so -lnsl /home/jwillia4/GRO/lib/libfftw3f.a -lm -Wl,--rpath -Wl,/home/jwillia4/GRO/lib -Wl,--rpath -Wl,/home/jwillia4/GRO/lib /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(main.o): In function `init_par': main.c:(.text+0xc0): undefined reference to `ompi_mpi_comm_world' main.c:(.text+0xc8): undefined reference to `ompi_mpi_comm_world' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(main.o): In function `init_multisystem': main.c:(.text+0xb99): undefined reference to `ompi_mpi_comm_world' main.c:(.text+0xbd9): undefined reference to `ompi_mpi_comm_world' main.c:(.text+0xbee): undefined reference to `ompi_mpi_comm_world' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):network.c:(.text+0x15): more undefined references to `ompi_mpi_comm_world' follow /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumi_sim': network.c:(.text+0x96): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x9b): undefined reference to `ompi_mpi_int' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumf_sim': network.c:(.text+0x4e6): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x4eb): undefined reference to `ompi_mpi_float' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumd_sim': network.c:(.text+0x9a6): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x9ab): undefined reference to `ompi_mpi_double' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumi': network.c:(.text+0xe8f): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0xe94): undefined reference to `ompi_mpi_int' network.c:(.text+0xec0): undefined reference to `ompi_mpi_int' network.c:(.text+0xed7): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0xedc): undefined reference to `ompi_mpi_int' network.c:(.text+0x12fe): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1303): undefined reference to `ompi_mpi_int' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumf': network.c:(.text+0x134e): undefined reference to `ompi_mpi_float' network.c:(.text+0x1354): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1380): undefined reference to `ompi_mpi_float' network.c:(.text+0x1397): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x139c): undefined reference to `ompi_mpi_float' network.c:(.text+0x183e): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1843): undefined reference to `ompi_mpi_float' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumd': network.c:(.text+0x1890): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1895): undefined reference to `ompi_mpi_double' network.c:(.text+0x18c2): undefined reference to `ompi_mpi_double' network.c:(.text+0x18d7): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x18dc): undefined reference to `ompi_mpi_double' network.c:(.text+0x1d86): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1d8b): undefined reference to `ompi_mpi_double'
Re: [gmx-users] compiling error in tools
Jennifer Williams wrote: Hello I know this is possibly an issue for the IT support at my Uni but I was wondering if someone could shed some light on what may have gone wrong so at least I can point them in the right direction. As I am getting very small diffusion coefficients when using g_msd, I want to increase the number of decimal points the diffusion coefficient is displayed to. In the file gmx_msd.c within src/tools I changed fprintf(out,# D[%10s] = %.4f (+/- %.4f) (1e-5 cm^2/s)\n, to fprintf(out,# D[%10s] = %.8f (+/- %.8f) (1e-5 cm^2/s)\n, then, as I have always done, I just typed in make g_msd to recompile this tool. I get the following error message: src/tools make g_msd mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\/home/jwillia4/GRO/share/top\ -I/home/jwillia4/GRO/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT g_msd.o -MD -MP -MF .deps/g_msd.Tpo -c -o g_msd.o g_msd.c mv -f .deps/g_msd.Tpo .deps/g_msd.Po /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/home/jwillia4/GRO/lib -lgslcblas -o g_msd g_msd.o libgmxana_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la -lgsl -lnsl -lfftw3f -lm mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o g_msd g_msd.o -L/home/jwillia4/GRO/lib ./.libs/libgmxana_mpi.a /home/jwillia4/GRO/gromacs-4.0.7/src/mdlib/.libs/libmd_mpi.a ../mdlib/.libs/libmd_mpi.a /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a ../gmxlib/.libs/libgmx_mpi.a /home/jwillia4/GRO/lib/libgslcblas.so /home/jwillia4/GRO/lib/libgsl.so -lnsl /home/jwillia4/GRO/lib/libfftw3f.a -lm -Wl,--rpath -Wl,/home/jwillia4/GRO/lib -Wl,--rpath -Wl,/home/jwillia4/GRO/lib /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(main.o): In function `init_par': main.c:(.text+0xc0): undefined reference to `ompi_mpi_comm_world' main.c:(.text+0xc8): undefined reference to `ompi_mpi_comm_world' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(main.o): In function `init_multisystem': main.c:(.text+0xb99): undefined reference to `ompi_mpi_comm_world' main.c:(.text+0xbd9): undefined reference to `ompi_mpi_comm_world' main.c:(.text+0xbee): undefined reference to `ompi_mpi_comm_world' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):network.c:(.text+0x15): more undefined references to `ompi_mpi_comm_world' follow /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumi_sim': network.c:(.text+0x96): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x9b): undefined reference to `ompi_mpi_int' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumf_sim': network.c:(.text+0x4e6): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x4eb): undefined reference to `ompi_mpi_float' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumd_sim': network.c:(.text+0x9a6): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x9ab): undefined reference to `ompi_mpi_double' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumi': network.c:(.text+0xe8f): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0xe94): undefined reference to `ompi_mpi_int' network.c:(.text+0xec0): undefined reference to `ompi_mpi_int' network.c:(.text+0xed7): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0xedc): undefined reference to `ompi_mpi_int' network.c:(.text+0x12fe): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1303): undefined reference to `ompi_mpi_int' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumf': network.c:(.text+0x134e): undefined reference to `ompi_mpi_float' network.c:(.text+0x1354): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1380): undefined reference to `ompi_mpi_float' network.c:(.text+0x1397): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x139c): undefined reference to `ompi_mpi_float' network.c:(.text+0x183e): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1843): undefined reference to `ompi_mpi_float' /home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In function `gmx_sumd': network.c:(.text+0x1890): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1895): undefined reference to `ompi_mpi_double' network.c:(.text+0x18c2): undefined reference to `ompi_mpi_double' network.c:(.text+0x18d7): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x18dc): undefined reference to `ompi_mpi_double' network.c:(.text+0x1d86): undefined reference to `ompi_mpi_op_sum' network.c:(.text+0x1d8b): undefined reference to `ompi_mpi_double'
Re: [gmx-users] dipole moment
On 2011-01-25 14.51, Olga Ivchenko wrote: Dear gromacs users, I would like to ask if there is a possibility in gromacs to calculate dipole moment between two atoms. For example one from water and another one from ligand. best, Olga If you mean the combined dipole moment of a particular water and a ligand then you can do it with g_dipoles and an index file. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] segmentation fault while running eneconv
Dear all, I launched on my system a first simulation of 5 ns, then I prolonged it to 50 ns using tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr and then mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt Since my simulation was interrupted several times, every time I relaunched it simply doing: mdrun -s tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4 At the end of these simulations I obtained the following files: - md1_5ns.xtc and .edr: files obtained from the first MD of 5 ns long - md2_50ns.xtc and .edr: files obtained by prolonging the first MD until 50ns - md2_50ns_2.xtc and .edr: files obtained by restarting the previous dynamics that was interrupted before 50 ns - md2_50ns_3.xtc and .edr: same as before - md2_50ns_4.xtc and .edr: same as before After all these runs, I want to concatenate all the dynamics in order to have a single .xtc file md_50ns_tot and a single .edr file md_50ns_tot.edr. For the first, I used: trjcat -f md1_5ns.xtc md2_50ns.xtc md2_50ns_2.xtc md2_50ns_3.xtc md2_50ns_4.xtc -o md_50ns_tot.xtc and all worked fine: I obtained the output file with no errors (there are no errors also in the .log files) On the contrary, when I tried to do the same with eneconv: eneconv -f md1_5ns.edr md2_50ns.edr md2_50ns_2.edr md2_50ns_3.edr md2_50ns_4.edr -o md_50ns_tot.edr I obtained the following output: Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file Reading energy frame 1 time 100.000 Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file Reading energy frame 0 time0.000 Opened 2GH9openmod4_pH10_50ns_2.part0002.edr as double precision energy file Reading energy frame 0 time 14900.000 Opened 2GH9openmod4_pH10_50ns_3.part0003.edr as double precision energy file Reading energy frame 0 time 27800.000 Opened 2GH9openmod4_pH10_50ns_4.part0004.edr as double precision energy file Reading energy frame 0 time 38800.000 Summary of files and start times used: FileStart time - 2GH9openmod4_pH10_5ns.edr0.000 2GH9openmod4_pH10_50ns.edr0.000 2GH9openmod4_pH10_50ns_2.part0002.edr14900.000 2GH9openmod4_pH10_50ns_3.part0003.edr27800.000 2GH9openmod4_pH10_50ns_4.part0004.edr38800.000 Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file Segmentation fault Looking for some hints in the gmx-users list the only thing I found that could be similar to my problem is this old message: http://lists.gromacs.org/pipermail/gmx-users/2007-January/025657.html I see in the output error message that the start time for the first two simulations is the same: could be this one the problem for my system? However, I did use tpbconv each time to make restarts of my simulations, I really don't know why the start time is 0.000 in the first two cases. Is there a problem in the results of simulations if these two simulations have the same start time? Practically, what can I do to concatenate my .edr files? Many thanks in advance and best regards Anna Marabotti Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with a gun is a dead man -- 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] segmentation fault while running eneconv
Anna Marabotti wrote: Dear all, I launched on my system a first simulation of 5 ns, then I prolonged it to 50 ns using tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr and then mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt Since my simulation was interrupted several times, every time I relaunched it simply doing: mdrun -s tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4 At the end of these simulations I obtained the following files: - md1_5ns.xtc and .edr: files obtained from the first MD of 5 ns long - md2_50ns.xtc and .edr: files obtained by prolonging the first MD until 50ns - md2_50ns_2.xtc and .edr: files obtained by restarting the previous dynamics that was interrupted before 50 ns - md2_50ns_3.xtc and .edr: same as before - md2_50ns_4.xtc and .edr: same as before After all these runs, I want to concatenate all the dynamics in order to have a single .xtc file md_50ns_tot and a single .edr file md_50ns_tot.edr. For the first, I used: trjcat -f md1_5ns.xtc md2_50ns.xtc md2_50ns_2.xtc md2_50ns_3.xtc md2_50ns_4.xtc -o md_50ns_tot.xtc and all worked fine: I obtained the output file with no errors (there are no errors also in the .log files) On the contrary, when I tried to do the same with eneconv: eneconv -f md1_5ns.edr md2_50ns.edr md2_50ns_2.edr md2_50ns_3.edr md2_50ns_4.edr -o md_50ns_tot.edr I obtained the following output: Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file Reading energy frame 1 time 100.000 Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file Reading energy frame 0 time0.000 Opened 2GH9openmod4_pH10_50ns_2.part0002.edr as double precision energy file Reading energy frame 0 time 14900.000 Opened 2GH9openmod4_pH10_50ns_3.part0003.edr as double precision energy file Reading energy frame 0 time 27800.000 Opened 2GH9openmod4_pH10_50ns_4.part0004.edr as double precision energy file Reading energy frame 0 time 38800.000 Summary of files and start times used: FileStart time - 2GH9openmod4_pH10_5ns.edr0.000 2GH9openmod4_pH10_50ns.edr0.000 2GH9openmod4_pH10_50ns_2.part0002.edr14900.000 2GH9openmod4_pH10_50ns_3.part0003.edr27800.000 2GH9openmod4_pH10_50ns_4.part0004.edr38800.000 Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file Segmentation fault Looking for some hints in the gmx-users list the only thing I found that could be similar to my problem is this old message: http://lists.gromacs.org/pipermail/gmx-users/2007-January/025657.html What Gromacs version are you using? If it is not 4.5.3, then you're probably running into a bug regarding double precision .edr files that was fixed some time ago. I see in the output error message that the start time for the first two simulations is the same: could be this one the problem for my system? However, I did use tpbconv each time to make restarts of my simulations, I really don't know why the start time is 0.000 in the first two cases. Well, your commands don't agree with the output of eneconv. The names are different. Perhaps you've confused what files you think you're using, or otherwise attempted to append to a file and then gave it a new name. In any case, gmxcheck is your friend here. Is there a problem in the results of simulations if these two simulations have the same start time? Practically, what can I do to concatenate my .edr files? Presumably, yes. As long as the .edr files have no internal corruptions (which, unfortunately, is quite possible if the job frequently went down), then you should be able to concatenate them. That also depends on the version of Gromacs you're using, if you're running into the old bug. It's always helpful to state right up front which version you're using when reporting a problem. -Justin Many thanks in advance and best regards Anna Marabotti Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it mailto:anna.marabo...@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with a gun is a dead man -- 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
Re: [gmx-users] dipole moment
Dear David, I mean a dipole moment between a particle atom in a ligand and a particular atom in water molecule. G_dipoles works for molecules, as I understood, not for atoms. best, Olga 2011/1/25 David van der Spoel sp...@xray.bmc.uu.se On 2011-01-25 14.51, Olga Ivchenko wrote: Dear gromacs users, I would like to ask if there is a possibility in gromacs to calculate dipole moment between two atoms. For example one from water and another one from ligand. best, Olga If you mean the combined dipole moment of a particular water and a ligand then you can do it with g_dipoles and an index file. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dipole moment
On 2011-01-25 16.01, Olga Ivchenko wrote: Dear David, I mean a dipole moment between a particle atom in a ligand and a particular atom in water molecule. G_dipoles works for molecules, as I understood, not for atoms. You can measure the distance between them, the dipole moment will be ill-defined unless the two atoms together have a zero charge. best, Olga 2011/1/25 David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se On 2011-01-25 14.51, Olga Ivchenko wrote: Dear gromacs users, I would like to ask if there is a possibility in gromacs to calculate dipole moment between two atoms. For example one from water and another one from ligand. best, Olga If you mean the combined dipole moment of a particular water and a ligand then you can do it with g_dipoles and an index file. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] dipole moment
Thank you David, Olga 2011/1/25 David van der Spoel sp...@xray.bmc.uu.se On 2011-01-25 16.01, Olga Ivchenko wrote: Dear David, I mean a dipole moment between a particle atom in a ligand and a particular atom in water molecule. G_dipoles works for molecules, as I understood, not for atoms. You can measure the distance between them, the dipole moment will be ill-defined unless the two atoms together have a zero charge. best, Olga 2011/1/25 David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se On 2011-01-25 14.51, Olga Ivchenko wrote: Dear gromacs users, I would like to ask if there is a possibility in gromacs to calculate dipole moment between two atoms. For example one from water and another one from ligand. best, Olga If you mean the combined dipole moment of a particular water and a ligand then you can do it with g_dipoles and an index file. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umbrella Sampling for a single molecule
Hi, I am interested in carrying out umbrella sampling for a protein in explicit solvent with the charmm forcefield. I want to impose a harmonic potential in the dihedral space of only some specific atoms in the protein molecule. I am having trouble figuring out a way to apply this using gromacs. Can I get some help on this? Thanks Pooja p.s. I have seen the tutorial on US by Justin but I am not sure if that is applicable to a single molecule when the purpose is to obtain the free-energy function associated with the transition in dihedral angles of specific some atoms in a protein molecule -- Quaerendo Invenietis-Seek and you shall discover. -- 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] Umbrella Sampling for a single molecule
Sai Pooja wrote: Hi, I am interested in carrying out umbrella sampling for a protein in explicit solvent with the charmm forcefield. I want to impose a harmonic potential in the dihedral space of only some specific atoms in the protein molecule. I am having trouble figuring out a way to apply this using gromacs. Can I get some help on this? http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints You'll have to build various configurations that correspond to different dihedral angles (which form the sampling windows), then restrain them. The energy attributed to the restraints is then stored in the .edr file. From these energies, you should be able to construct the energy curve over the sampling windows. There are examples of this in the literature, so I suspect you should be able to find some demonstrations of how it's applied. -Justin Thanks Pooja p.s. I have seen the tutorial on US by Justin but I am not sure if that is applicable to a single molecule when the purpose is to obtain the free-energy function associated with the transition in dihedral angles of specific some atoms in a protein molecule -- Quaerendo Invenietis-Seek and you shall discover. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: segmentation fault while running eneconv
Dear Justin, thank you for your answer. I'm currently using Gromacs version 4.0.7 which was compiled in double precision, therefore I strongly suspect that this is a problem linked to the old bug. It seems to me that I used eneconv previously on this machine to concatenate .edr files, but I cannot be sure. However, before writing you I copied the .edr files on another machine, which still has Gromacs 4.0.7 installed, but compiled in single precision, and still I found the same error Segmentation fault. Concerning the name of the files, when I described the commands in my previous message I used a simplified version of their names in order to avoid writing the long 2GH9openmod4_pH...blabla, but I checked several times the names I used and I can assure you that I tried to concatenate the correct file names. Therefore, the problem is not a typo. Sorry for not explaining it before. I made a check wit gmxcheck on 2 files: the .edr and .xtc files from the MD of 5 ns and the .edr and .xtc files from the MD of 50 ns (started immediately after the 5ns using tpbconv): these are the results: Checking file 2GH9openmod4_pH10_5ns.xtc Reading frame 0 time0.000 # Atoms 40139 Precision 0.001 (nm) Last frame 1000 time 5000.000 Item#frames Timestep (ps) Step 10015 Time 10015 Lambda 0 Coords10015 Velocities 0 Forces 0 Box 10015 Checking energy file 2GH9openmod4_pH10_5ns.edr Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 50 time 5000.000 Found 51 frames with a timestep of 100 ps. Checking file 2GH9openmod4_pH10_50ns.xtc Reading frame 0 time0.000 # Atoms 40139 Precision 0.001 (nm) Reading frame2000 time 1.000 Item#frames Timestep (ps) Step 29815 Time 29815 Lambda 0 Coords29815 Velocities 0 Forces 0 Box 29815 Checking energy file 2GH9openmod4_pH10_50ns.edr Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 149 time 14900.000 Found 150 frames with a timestep of 100 ps. It seems to me that all is regular; the only strange thing is that both start at time 0, despite I used tpbconv+mdrun with cpi to continue the MD after the first 5 ns. I return with my previous question: how can I manage this problem, especially if I have the version 4.0.7? Do I have to ask administrators to fix the bug? Do I have to restart all my simulations? Thank you very much and best regards Anna -- Message: 1 Date: Tue, 25 Jan 2011 09:43:20 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] segmentation fault while running eneconv To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d3ee188.7000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear all, I launched on my system a first simulation of 5 ns, then I prolonged it to 50 ns using tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr and then mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt Since my simulation was interrupted several times, every time I relaunched it simply doing: mdrun -s tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4 At the end of these simulations I obtained the following files: - md1_5ns.xtc and .edr: files obtained from the first MD of 5 ns long - md2_50ns.xtc and .edr: files obtained by prolonging the first MD until 50ns - md2_50ns_2.xtc and .edr: files obtained by restarting the previous dynamics that was interrupted before 50 ns - md2_50ns_3.xtc and .edr: same as before - md2_50ns_4.xtc and .edr: same as before After all these runs, I want to concatenate all the dynamics in order to have a single .xtc file md_50ns_tot and a single .edr file md_50ns_tot.edr. For the first, I used: trjcat -f md1_5ns.xtc md2_50ns.xtc md2_50ns_2.xtc md2_50ns_3.xtc md2_50ns_4.xtc -o md_50ns_tot.xtc and all worked fine: I obtained the output file with no errors (there are no errors also in the .log files) On the contrary, when I tried to do the same with eneconv: eneconv -f md1_5ns.edr md2_50ns.edr md2_50ns_2.edr md2_50ns_3.edr md2_50ns_4.edr -o md_50ns_tot.edr I obtained the following output: Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file Reading energy frame 1 time 100.000 Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file Reading energy frame 0 time0.000 Opened 2GH9openmod4_pH10_50ns_2.part0002.edr as double precision energy file Reading energy frame 0 time 14900.000 Opened 2GH9openmod4_pH10_50ns_3.part0003.edr as double precision energy file Reading energy frame 0 time 27800.000 Opened 2GH9openmod4_pH10_50ns_4.part0004.edr as double precision energy
Re: [gmx-users] Re: Secondary structure loss in implicit solvent simulations
OK, that is what I was trying to figure out -- is the problem reproducible on both GPU and CPU. Now, you havent answered the direct question, if the energies are the same for at least the first 5 steps are so -- without that knowledge, then here might be different errors occurring in GPU vs CPU. At this point, the question is then whether this works with another code with the same input parameters. Sander (part of the AmberTools system)is downloadable (I believe to anyone, not just academics), so you can try running the same system on Sander, using the best fit to the implicit solvent model in gromacs. If THAT works, and Gromacs GPU fails, then it would appear to be a problem with Gromacs implicit solvent implementation, and should be posted to redmine as a bug, as well as described on the list with full details (more than you have provided so far!) so that it can be reproduced by the developers. Best, On Tue, Jan 25, 2011 at 5:05 AM, K. Singhal k.sing...@uva.nl wrote: Hi It's not necessarily GPU-specific, it's implicit solvent-specific. I don't get these problems in explicit solvent simulations on CPU, only in implicit solvent simulations both on GPU as well as CPU. One of the problems that I can think of is unbalanced charges that I would have balanced out using NaCl ions, but not any more. Regards Kush -- Kushagra Singhal Promovendus, Computational Chemistry van 't Hoff Institute of Molecular Sciences Science Park 904, room C2.119 1098 XH Amsterdam, The Netherlands +31 205256965 Universiteit van Amsterdam k.sing...@uva.nl -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: segmentation fault while running eneconv
anna.marabo...@isa.cnr.it wrote: Dear Justin, thank you for your answer. I'm currently using Gromacs version 4.0.7 which was compiled in double precision, therefore I strongly suspect that this is a problem linked to the old bug. It seems to me that I used eneconv previously on this machine to concatenate .edr files, but I cannot be sure. However, before writing you I copied the .edr files on another machine, which still has Gromacs 4.0.7 installed, but compiled in single precision, and still I found the same error Segmentation fault. I don't believe you have a problem related to the bug; it was introduced in the 4.5 series, so 4.0.7 should be unaffected. Since gmxcheck seems to have worked, that's more evidence that there is no bug. The problem was in the .edr formating, causing all Gromacs utilities to stop reading double-precision .edr files. Concerning the name of the files, when I described the commands in my previous message I used a simplified version of their names in order to avoid writing the long 2GH9openmod4_pH...blabla, but I checked several times the names I used and I can assure you that I tried to concatenate the correct file names. Therefore, the problem is not a typo. Sorry for not explaining it before. OK. Literal is always better, and often requires a simple cut and paste from the terminal, rather than any manual typing at all :) I made a check wit gmxcheck on 2 files: the .edr and .xtc files from the MD of 5 ns and the .edr and .xtc files from the MD of 50 ns (started immediately after the 5ns using tpbconv): these are the results: Checking file 2GH9openmod4_pH10_5ns.xtc Reading frame 0 time0.000 # Atoms 40139 Precision 0.001 (nm) Last frame 1000 time 5000.000 Item#frames Timestep (ps) Step 10015 Time 10015 Lambda 0 Coords10015 Velocities 0 Forces 0 Box 10015 Checking energy file 2GH9openmod4_pH10_5ns.edr Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 50 time 5000.000 Found 51 frames with a timestep of 100 ps. Checking file 2GH9openmod4_pH10_50ns.xtc Reading frame 0 time0.000 # Atoms 40139 Precision 0.001 (nm) Reading frame2000 time 1.000 Item#frames Timestep (ps) Step 29815 Time 29815 Lambda 0 Coords29815 Velocities 0 Forces 0 Box 29815 Checking energy file 2GH9openmod4_pH10_50ns.edr Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 149 time 14900.000 Found 150 frames with a timestep of 100 ps. It seems to me that all is regular; the only strange thing is that both start at time 0, despite I used tpbconv+mdrun with cpi to continue the MD after the first 5 ns. What does the log file tell you regarding the outset of the second job? It should say that it's starting from a checkpoint, and the first interval written should have a time of 5000 ps. If not, then the checkpoint file was not properly used. If both .edr files start at the same point, that could be a reason for the seg fault, but that's a bit of a guess. From the gmxcheck output, it appears that your _50ns.edr file does indeed start from 0 instead of 5000, as you would hope. I return with my previous question: how can I manage this problem, especially if I have the version 4.0.7? Do I have to ask administrators to fix the bug? Do I have to restart all my simulations? If the continuation instead started from t=0, then you don't have to re-do anything, just don't use the _5ns.* information (.xtc, .edr, etc) since you basically did that portion of the simulation over. The log files will tell you what's going on. -Justin Thank you very much and best regards Anna -- Message: 1 Date: Tue, 25 Jan 2011 09:43:20 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] segmentation fault while running eneconv To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d3ee188.7000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear all, I launched on my system a first simulation of 5 ns, then I prolonged it to 50 ns using tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr and then mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt Since my simulation was interrupted several times, every time I relaunched it simply doing: mdrun -s tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4 At the end of these simulations I obtained the following files: - md1_5ns.xtc and .edr: files obtained from the first MD of 5 ns long - md2_50ns.xtc and .edr: files obtained by prolonging the first MD until 50ns - md2_50ns_2.xtc and .edr: files obtained by restarting the previous
[gmx-users] Two machines, same job, one fails
Hi all, I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and FFTW 3.2.2. My iMac will run the job (over 4000 steps, till I killed it) at 4fs steps. (I am using heavy H) Once I put this on our groups AMD Cluster the jobs fail even with 2fs steps. (with thousands of lincs errors) We have recompiled the clusters gromacs 4.5.3 build, with no change. I know the system is the same since I copied the job from the server to my machine, to rerun it. What is going on? Why can one machine run a job perfectly and the other cannot? I also know there is adequate memory on both machines. Below is my command sequence: echo == date RNAP-C.joblog echo g453s-grompp -f em.mdp -c RNAP-C_b4em.gro -p RNAP-C.top -o RNAP-C_em.tpr /share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f em.mdp -c RNAP-C_b4em.gro -p RNAP-C.top -o RNAP-C_em.tpr date RNAP-C.joblog echo g453s-mdrun -v -s RNAP-C_em.tpr -c RNAP-C_after_em.gro -g emlog.log -cpo state_em.cpt -nt 2 /share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_em.tpr -c RNAP-C_after_em.gro -g emlog.log -cpo stat_em.cpt -nt 2 date RNAP-C.joblog echo g453s-grompp -f pr.mdp -c RNAP-C_after_em.gro -p RNAP-C.top -o RNAP-C_pr.tpr /share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f pr.mdp -c RNAP-C_after_em.gro -p RNAP-C.top -o RNAP-C_pr.tpr echo g453s-mdrun -v -s RNAP-C_pr.tpr -e pr.edr -c RNAP-C_after_pr.gro -g prlog.log -cpo state_pr.cpt -nt 2 -dhdl dhdl-pr.xvg /share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_pr.tpr -e pr.edr -c RNAP-C_after_pr.gro -g prlog.log -cpo state_pr.cpt -nt 2 -dhdl dhdl-pr.xvg date RNAP-C.joblog echo g453s-grompp -f md.mdp -c RNAP-C_after_pr.gro -p RNAP-C.top -o RNAP-C_md.tpr /share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f md.mdp -c RNAP-C_after_pr.gro -p RNAP-C.top -o RNAP-C_md.tpr date RNAP-C.joblog echo g453s-mdrun -v -s RNAP-C_md.tpr -o RNAP-C_md.trr -c RNAP-C_after_md.gro -g md.log -e md.edr -cpo state_md.cpt -nt 2 -dhdl dhdl-md.xvg /share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_md.tpr -o RNAP-C_md.trr -c RNAP-C_after_md.gro -g md.log -e md.edr -cpo state_md.cpt -nt 2 -dhdl dhdl-md.xvg date RNAP-C.joblog echo g453s-grompp -f FEP.mdp -c RNAP-C_after_md.gro -p RNAP-C.top -o RNAP-C_fep.tpr /share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f FEP.mdp -c RNAP-C_after_md.gro -p RNAP-C.top -o RNAP-C_fep.tpr date RNAP-C.joblog echo g453s-mdrun -v -s RNAP-C_fep.tpr -o RNAP-C_fep.trr -c RNAP-C_after_fep.gro -g fep.log -e fep.edr -cpo state_fep.cpt -nt 2 -dhdl dhdl-fep.xvg /share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_fep.tpr -o RNAP-C_fep.trr -c RNAP-C_after_fep.gro -g fep.log -e fep.edr -cpo state_fep.cpt -nt 2 -dhdl dhdl-fep.xvg I can add my .mdps but I do not think they are the problem since I know it works on my personal iMac. Thank you, TJ Mustard Email: musta...@onid.orst.edu -- 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] nstcomm nstcalcenergy defeats the purpose of nstcalcenergy
Dear users, How can I fixed the NOTE the following? Will this note/warning cause a problem in the calculations?What is the meaning of this note? NOTE 1 [file pr.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun_mpi executable not found
Alright. So meaning I should have instead issued: ./configure --enable-mpi --program-suffix=_mpi make mdrun make install-mdrun make links to have installed an MPI-enabled executable called mdrun_mpi apart from the existing mdrun executable? (Would I also need to append the _mpi suffix when issuing the first two make and make install commands above? Thanks, Justin On Mon, Jan 24, 2011 at 8:08 PM, Justin A. Lemkul jalem...@vt.edu wrote: Justin Kat wrote: Thank you for the reply! hmm mdrun_mpi does not appear in the list of executables in /usr/local/gromacs/bin (and well therefore not in /usr/local/bin). Which set of installation commands that I used should have compiled the mdrun_mpi executable? And how should I go about getting the mdrun_mpi executable at this point? I see it now. When you configured with --enable-mpi, you didn't specify --program-suffix=_mpi, so the installation procedure over-wrote your existing (serial) mdrun with an MPI-enabled one simply called mdrun. The configure output should have warned you about this. You could, in theory, simply re-name your existing executable mdrun_mpi and then re-install a serial mdrun, if you need it. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] nstcomm nstcalcenergy defeats the purpose of nstcalcenergy
On 26/01/2011 8:10 AM, ahmet yıldırım wrote: Dear users, How can I fixed the NOTE the following? Will this note/warning cause a problem in the calculations?What is the meaning of this note? NOTE 1 [file pr.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy Did you look these definitions up in the manual before firing off an email? :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun_mpi executable not found
On 26/01/2011 8:50 AM, Justin Kat wrote: Alright. So meaning I should have instead issued: ./configure --enable-mpi --program-suffix=_mpi|| make mdrun make install-mdrun make links to have installed an MPI-enabled executable called mdrun_mpi apart from the existing mdrun executable? (Would I also need to append the _mpi suffix when issuing the first two make and make install commands above? No. See http://www.gromacs.org/Downloads/Installation_Instructions Mark Thanks, Justin On Mon, Jan 24, 2011 at 8:08 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Justin Kat wrote: Thank you for the reply! hmm mdrun_mpi does not appear in the list of executables in /usr/local/gromacs/bin (and well therefore not in /usr/local/bin). Which set of installation commands that I used should have compiled the mdrun_mpi executable? And how should I go about getting the mdrun_mpi executable at this point? I see it now. When you configured with --enable-mpi, you didn't specify --program-suffix=_mpi, so the installation procedure over-wrote your existing (serial) mdrun with an MPI-enabled one simply called mdrun. The configure output should have warned you about this. You could, in theory, simply re-name your existing executable mdrun_mpi and then re-install a serial mdrun, if you need it. -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 -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97
On 26/01/2011 12:05 AM, Justin A. Lemkul wrote: gromacs wrote: HI Friends, I get the following note, The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. I want to keep the T at 300K, so does it matter to select any thermostat method? The choice of thermostat certainly does matter, otherwise you wouldn't get this note. Refer to the numerous discussions in the list archive as to why one would or would not (usually) use the Berendsen thermostat, as well as: http://www.gromacs.org/Documentation/Terminology/Thermostats http://www.gromacs.org/Documentation/Terminology/Berendsen ... and the relevant manual sections. Mark Another note when i use PME: Estimate for the relative computational load of the PME mesh part: 0.97 NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing So what is the reason? I use type=PME Your combination of settings (rcoulomb, fourierspacing, and perhaps a few others) indicate that your simulation is going to spend an inordinate amount of time doing PME calculations, so your performance will suffer. Seeing your entire .mdp file would be necessary if you want further guidance. -Justin Is my setting proper? 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] Two machines, same job, one fails
On 26/01/2011 5:50 AM, TJ Mustard wrote: Hi all, I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and FFTW 3.2.2. My iMac will run the job (over 4000 steps, till I killed it) at 4fs steps. (I am using heavy H) Once I put this on our groups AMD Cluster the jobs fail even with 2fs steps. (with thousands of lincs errors) We have recompiled the clusters gromacs 4.5.3 build, with no change. I know the system is the same since I copied the job from the server to my machine, to rerun it. What is going on? Why can one machine run a job perfectly and the other cannot? I also know there is adequate memory on both machines. You've posted this before, and I made a number of diagnostic suggestions. What did you learn? Mark Below is my command sequence: echo == date RNAP-C.joblog echo g453s-grompp -f em.mdp -c RNAP-C_b4em.gro -p RNAP-C.top -o RNAP-C_em.tpr /share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f em.mdp -c RNAP-C_b4em.gro -p RNAP-C.top -o RNAP-C_em.tpr date RNAP-C.joblog echo g453s-mdrun -v -s RNAP-C_em.tpr -c RNAP-C_after_em.gro -g emlog.log -cpo state_em.cpt -nt 2 /share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_em.tpr -c RNAP-C_after_em.gro -g emlog.log -cpo stat_em.cpt -nt 2 date RNAP-C.joblog echo g453s-grompp -f pr.mdp -c RNAP-C_after_em.gro -p RNAP-C.top -o RNAP-C_pr.tpr /share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f pr.mdp -c RNAP-C_after_em.gro -p RNAP-C.top -o RNAP-C_pr.tpr echo g453s-mdrun -v -s RNAP-C_pr.tpr -e pr.edr -c RNAP-C_after_pr.gro -g prlog.log -cpo state_pr.cpt -nt 2 -dhdl dhdl-pr.xvg /share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_pr.tpr -e pr.edr -c RNAP-C_after_pr.gro -g prlog.log -cpo state_pr.cpt -nt 2 -dhdl dhdl-pr.xvg date RNAP-C.joblog echo g453s-grompp -f md.mdp -c RNAP-C_after_pr.gro -p RNAP-C.top -o RNAP-C_md.tpr /share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f md.mdp -c RNAP-C_after_pr.gro -p RNAP-C.top -o RNAP-C_md.tpr date RNAP-C.joblog echo g453s-mdrun -v -s RNAP-C_md.tpr -o RNAP-C_md.trr -c RNAP-C_after_md.gro -g md.log -e md.edr -cpo state_md.cpt -nt 2 -dhdl dhdl-md.xvg /share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_md.tpr -o RNAP-C_md.trr -c RNAP-C_after_md.gro -g md.log -e md.edr -cpo state_md.cpt -nt 2 -dhdl dhdl-md.xvg date RNAP-C.joblog echo g453s-grompp -f FEP.mdp -c RNAP-C_after_md.gro -p RNAP-C.top -o RNAP-C_fep.tpr /share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f FEP.mdp -c RNAP-C_after_md.gro -p RNAP-C.top -o RNAP-C_fep.tpr date RNAP-C.joblog echo g453s-mdrun -v -s RNAP-C_fep.tpr -o RNAP-C_fep.trr -c RNAP-C_after_fep.gro -g fep.log -e fep.edr -cpo state_fep.cpt -nt 2 -dhdl dhdl-fep.xvg /share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_fep.tpr -o RNAP-C_fep.trr -c RNAP-C_after_fep.gro -g fep.log -e fep.edr -cpo state_fep.cpt -nt 2 -dhdl dhdl-fep.xvg I can add my .mdps but I do not think they are the problem since I know it works on my personal iMac. Thank you, TJ Mustard Email: musta...@onid.orst.edu -- 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] Two machines, same job, one fails
On January 25, 2011 at 2:08 PM Mark Abraham mark.abra...@anu.edu.au wrote: On 26/01/2011 5:50 AM, TJ Mustard wrote: Hi all, I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and FFTW 3.2.2. My iMac will run the job (over 4000 steps, till I killed it) at 4fs steps. (I am using heavy H) Once I put this on our groups AMD Cluster the jobs fail even with 2fs steps. (with thousands of lincs errors) We have recompiled the clusters gromacs 4.5.3 build, with no change. I know the system is the same since I copied the job from the server to my machine, to rerun it. What is going on? Why can one machine run a job perfectly and the other cannot? I also know there is adequate memory on both machines. Youve posted this before, and I made a number of diagnostic suggestions. What did you learn? Mark Mark and all, First thank you for all our help. What you suggested last time helped considerably with our jobs/calculations. I have learned that using the standard mdp settings allow my heavyh 4fs jobs to run on my iMac (intel) and have made these my new standard for future jobs. We chose to use the smaller 0.8nm PME/Cutoff due to others papers/tutorials, but now we understand why we need these standard settings. Now what I see to be our problem is that our machines have some sort of variable we cannot account for. If I am blind to my error, please show me. I just dont understand why one computer works while the other does not. We have recompiled gromacs 4.5.3 single precission on our cluster, and still have this problem. Now I understand that my iMac works, but it only has 2 cpus and the cluster has 320. Since we are running our jobs via a Bennets Acceptance Ratio FEP with 21 lambda windows, using just one 2 cpu machine would take too long. Especially since we wish to start pseudo high throughput drug testing. In my .mdp files now, the only changes are: (the default setting is on the right of the ;) define = ; = ; RUN CONTROL PARAMETERS integrator = sd ; = md ; Start time and timestep in ps tinit = 0 ; = 0 dt = 0.004 ; = 0.001 nsteps = 75 ; = 0 (this one depends on the window and particular part of our job) ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 ; = 100 (to save on disk space) nstvout = 1 ; = 100 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME ; = Cutoff rcoulomb-switch = 0 ; = 0 rcoulomb = 1 ; = 1 ; Relative dielectric constant for the medium and the reaction field epsilon_r = 1 ; = 1 epsilon_rf = 1 ; = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; = Cut-off ; cut-off lengths rvdw-switch = 0 ; = 0 rvdw = 1 ; = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; = 0.12 ; EWALD/PME/PPPM parameters pme_order = 4 ; = 4 ewald_rtol = 1e-05 ; = 1e-05 ewald_geometry = 3d ; = 3d epsilon_surface = 0 ; = 0 optimize_fft = yes ; = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = v-rescale ; = No nsttcouple = -1 ; = -1 nh-chain-length = 10 ; = 10 ; Groups to couple separately tc-grps = System ; = ; Time constant (ps) and reference temperature (K) tau-t = 0.1 ; = ref-t = 300 ; = ; Pressure coupling Pcoupl = Parrinello-Rahman ; = No Pcoupltype = Isotropic nstpcouple = -1 ; = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p = 1 ; = 1 compressibility = 4.5e-5 ; = ref-p = 1.0 ; = ; OPTIONS FOR BONDS constraints = all-bonds ; = none ; Type of constraint algorithm constraint-algorithm = Lincs ; = Lincs ; Free energy control stuff free-energy = yes ; = no init-lambda = 0.00 ; = 0 delta-lambda = 0 ; = 0 foreign_lambda = 0.05 ; = sc-alpha = 0.5 ; = 0 sc-power = 1.0 ; = 0 sc-sigma = 0.3 ; = 0.3 nstdhdl = 1 ; = 10 separate-dhdl-file = yes ; = yes dhdl-derivatives = yes ; = yes dh_hist_size = 0 ; = 0 dh_hist_spacing = 0.1 ; = 0.1 couple-moltype = LGD ; = couple-lambda0 = vdw-q ; = vdw-q couple-lambda1 = none ; = vdw-q couple-intramol = no ; = no Some of these change due to positional restraint md and energy minimization. All of these settings have come from either tutorials, papers or peoples advice. If it would be advantageous I can post my entire energy minimization, positional restraint, md, and FEP mdp files. Thank you, TJ Mustard
Re: [gmx-users] Two machines, same job, one fails
TJ Mustard wrote: On January 25, 2011 at 2:08 PM Mark Abraham mark.abra...@anu.edu.au wrote: On 26/01/2011 5:50 AM, TJ Mustard wrote: Hi all, I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and FFTW 3.2.2. My iMac will run the job (over 4000 steps, till I killed it) at 4fs steps. (I am using heavy H) Once I put this on our groups AMD Cluster the jobs fail even with 2fs steps. (with thousands of lincs errors) We have recompiled the clusters gromacs 4.5.3 build, with no change. I know the system is the same since I copied the job from the server to my machine, to rerun it. What is going on? Why can one machine run a job perfectly and the other cannot? I also know there is adequate memory on both machines. You've posted this before, and I made a number of diagnostic suggestions. What did you learn? Mark Mark and all, First thank you for all our help. What you suggested last time helped considerably with our jobs/calculations. I have learned that using the standard mdp settings allow my heavyh 4fs jobs to run on my iMac (intel) and have made these my new standard for future jobs. We chose to use the smaller 0.8nm PME/Cutoff due to others papers/tutorials, but now we understand why we need these standard settings. Now what I see to be our problem is that our machines have some sort of variable we cannot account for. If I am blind to my error, please show me. I just don't understand why one computer works while the other does not. We have recompiled gromacs 4.5.3 single precission on our cluster, and still have this problem. I know the feeling all too well. PowerPC jobs crash instantly, on our cluster, despite working beautifully on our lab machines. There's a bug report about that one, but I haven't heard anything about AMD failures. It remains a possibility that something beyond your control is going on. To explore a bit further: 1. Do the systems in question crash immediately (i.e., step zero) or do they run for some time? 2. If they give you even a little bit of output, you can analyze which energy terms, etc go haywire with the tips listed here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System That would help in tracking down any potential bug or error. 3. Is it just the production runs that are crashing, or everything? If EM isn't even working, that smells even buggier. 4. Are the compilers the same on the iMac vs. AMD cluster? -Justin Now I understand that my iMac works, but it only has 2 cpus and the cluster has 320. Since we are running our jobs via a Bennet's Acceptance Ratio FEP with 21 lambda windows, using just one 2 cpu machine would take too long. Especially since we wish to start pseudo high throughput drug testing. In my .mdp files now, the only changes are: (the default setting is on the right of the ;) define = ; = ; RUN CONTROL PARAMETERS integrator = sd; = md ; Start time and timestep in ps tinit= 0; = 0 dt = 0.004; = 0.001 nsteps = 75 ; = 0 (this one depends on the window and particular part of our job) ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1; = 100 (to save on disk space) nstvout = 1; = 100 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME; = Cutoff rcoulomb-switch = 0; = 0 rcoulomb = 1 ; = 1 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1; = 1 epsilon_rf = 1; = 1 ; Method for doing Van der Waals vdw-type = Cut-off; = Cut-off ; cut-off lengths rvdw-switch = 0; = 0 rvdw = 1 ; = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12; = 0.12 ; EWALD/PME/PPPM parameters pme_order= 4; = 4 ewald_rtol = 1e-05; = 1e-05 ewald_geometry = 3d; = 3d epsilon_surface = 0; = 0 optimize_fft = yes; = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = v-rescale; = No nsttcouple = -1; = -1 nh-chain-length = 10; = 10 ; Groups to couple separately tc-grps = System; = ; Time constant (ps) and reference temperature (K) tau-t= 0.1; = ref-t= 300; = ; Pressure coupling Pcoupl = Parrinello-Rahman; = No Pcoupltype = Isotropic nstpcouple = -1; = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 1; = 1 compressibility =
[gmx-users] (no subject)
Dear Justin/Mark, I would like to have a private course about Gromacs in Holland. Is there such a facility for this? Who should I talk with? Or is there a workshop in near future? best wishes -- 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] Two machines, same job, one fails
On January 25, 2011 at 3:24 PM Justin A. Lemkul jalem...@vt.edu wrote: TJ Mustard wrote: On January 25, 2011 at 2:08 PM Mark Abraham mark.abra...@anu.edu.au wrote: On 26/01/2011 5:50 AM, TJ Mustard wrote: Hi all, I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and FFTW 3.2.2. My iMac will run the job (over 4000 steps, till I killed it) at 4fs steps. (I am using heavy H) Once I put this on our groups AMD Cluster the jobs fail even with 2fs steps. (with thousands of lincs errors) We have recompiled the clusters gromacs 4.5.3 build, with no change. I know the system is the same since I copied the job from the server to my machine, to rerun it. What is going on? Why can one machine run a job perfectly and the other cannot? I also know there is adequate memory on both machines. Youve posted this before, and I made a number of diagnostic suggestions. What did you learn? Mark Mark and all, First thank you for all our help. What you suggested last time helped considerably with our jobs/calculations. I have learned that using the standard mdp settings allow my heavyh 4fs jobs to run on my iMac (intel) and have made these my new standard for future jobs. We chose to use the smaller 0.8nm PME/Cutoff due to others papers/tutorials, but now we understand why we need these standard settings. Now what I see to be our problem is that our machines have some sort of variable we cannot account for. If I am blind to my error, please show me. I just dont understand why one computer works while the other does not. We have recompiled gromacs 4.5.3 single precission on our cluster, and still have this problem. I know the feeling all too well. PowerPC jobs crash instantly, on our cluster, despite working beautifully on our lab machines. Theres a bug report about that one, but I havent heard anything about AMD failures. It remains a possibility that something beyond your control is going on. To explore a bit further: 1. Do the systems in question crash immediately (i.e., step zero) or do they run for some time? Step 0, every time. 2. If they give you even a little bit of output, you can analyze which energy terms, etc go haywire with the tips listed here: All I have seen on these is LINCS Errors and Water molecules unable to be settled. But I will check this out right now, and email if I smell trouble. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System That would help in tracking down any potential bug or error. 3. Is it just the production runs that are crashing, or everything? If EM isnt even working, that smells even buggier. Awesome question here, we have seen some weird stuff. Sometimes the cluster will give us segmentation faults, then it will fail on our machines or sometimes not on our iMacs. I know weird! If EM starts on the cluster it will finish. Where we have issues is in positional restraint (PR) and MD and MD/FEP. It doesnt matter if FEP is on or off in a MD (although we are using SD for these MD/FEP runs). 4. Are the compilers the same on the iMac vs. AMD cluster? No I am using x86_64-apple-darwin10 GCC 4.4.4 and the cluster is using x86_64-redhat-linux 4.1.2 GCC. I just did a quick yum search and there doesnt seem to be a newer GCC. We know you are going to cmake but we have yet to get it implemented on our cluster successfully. Thank you, TJ Mustard -Justin Now I understand that my iMac works, but it only has 2 cpus and the cluster has 320. Since we are running our jobs via a Bennets Acceptance Ratio FEP with 21 lambda windows, using just one 2 cpu machine would take too long. Especially since we wish to start pseudo high throughput drug testing. In my .mdp files now, the only changes are: (the default setting is on the right of the ;) define = ; = ; RUN CONTROL PARAMETERS integrator = sd ; = md ; Start time and timestep in ps tinit = 0 ; = 0 dt = 0.004 ; = 0.001 nsteps = 75 ; = 0 (this
Re: [gmx-users] Need help troubleshooting an mdrun-gpu error message!
Hi, There are two things you should test: a) Does your NVIDIA driver + CUDA setup work? Try to run a different CUDA-based program, e.g. you can get the CUDA SDK and compile one of the simple programs like deviceQuery or bandwidthTest. b) If the above works, try to compile OpenMM from source with the same CUDA version as the one used when compiling Gromacs. Let me know if you succeed! Cheers, -- Szilárd On Tue, Jan 25, 2011 at 3:49 AM, Solomon Berman smber...@bu.edu wrote: Hello friends, I have installed mdrun-gpu v. 4.5.3 without incident on my group's computer with a suitable GPU. The computer uses a Linux OS. CUDA and OpenMM are installed in the usual places. I created the topol.tpr file with grompp v. 4.5.3, also without incident. When I run ./mdrun-gpu -v, the following error message is produced: Program mdrun-gpu, VERSION 4.5.3 Source code file: /home/smberman/sourcecode/gromacs-4.5.3/src/kernel/openmm_wrapper.cpp, line: 1259 Fatal error: The requested platform CUDA could not be found. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I have the following in my .bash_profile: export PATH=~/bin:~/usr/bin:~/usr/local/bin:/usr/local/cuda/bin:$PATH:. LD_LIBRARY_PATH=/usr/local/openmm/lib:/usr/local/cuda/lib export LD_LIBRARY_PATH I have run the available tests that came with the OpenMM library, and the CUDA tests pass. Could someone please explain what this error means and the appropriate way to remedy it? Thank you!! Best, Solomon Berman Chemistry Department Boston University -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Two machines, same job, one fails
On 01/26/11, TJ Mustard musta...@onid.orst.edu wrote: On January 25, 2011 at 3:24 PM Justin A. Lemkul jalem...@vt.edu wrote: TJ Mustard wrote: On January 25, 2011 at 2:08 PM Mark Abraham mark.abra...@anu.edu.au wrote: On 26/01/2011 5:50 AM, TJ Mustard wrote: Hi all, I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and FFTW 3.2.2. My iMac will run the job (over 4000 steps, till I killed it) at 4fs steps. (I am using heavy H) Once I put this on our groups AMD Cluster the jobs fail even with 2fs steps. (with thousands of lincs errors) We have recompiled the clusters gromacs 4.5.3 build, with no change. I know the system is the same since I copied the job from the server to my machine, to rerun it. What is going on? Why can one machine run a job perfectly and the other cannot? I also know there is adequate memory on both machines. You've posted this before, and I made a number of diagnostic suggestions. What did you learn? Mark Mark and all, First thank you for all our help. What you suggested last time helped considerably with our jobs/calculations. I have learned that using the standard mdp settings allow my heavyh 4fs jobs to run on my iMac (intel) and have made these my new standard for future jobs. We chose to use the smaller 0.8nm PME/Cutoff due to others papers/tutorials, but now we understand why we need these standard settings. Now what I see to be our problem is that our machines have some sort of variable we cannot account for. If I am blind to my error, please show me. I just don't understand why one computer works while the other does not. We have recompiled gromacs 4.5.3 single precission on our cluster, and still have this problem. I know the feeling all too well. PowerPC jobs crash instantly, on our cluster, despite working beautifully on our lab machines. There's a bug report about that one, but I haven't heard anything about AMD failures. It remains a possibility that something beyond your control is going on. To explore a bit further: 1. Do the systems in question crash immediately (i.e., step zero) or do they run for some time? Step 0, every time. 2. If they give you even a little bit of output, you can analyze which energy terms, etc go haywire with the tips listed here: All I have seen on these is LINCS Errors and Water molecules unable to be settled. But I will check this out right now, and email if I smell trouble. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System That would help in tracking down any potential bug or error. 3. Is it just the production runs that are crashing, or everything? If EM isn't even working, that smells even buggier. Awesome question here, we have seen some weird stuff. Sometimes the cluster will give us segmentation faults, then it will fail on our machines or sometimes not on our iMacs. I know weird! If EM starts on the cluster it will finish. Where we have issues is in positional restraint (PR) and MD and MD/FEP. It doesn't matter if FEP is on or off in a MD (although we are using SD for these MD/FEP runs). Good. That rules out FEP as the source of the problem, like I asked in your previous thread. 4. Are the compilers the same on the iMac vs. AMD cluster? No I am using x86_64-apple-darwin10 GCC 4.4.4 and the cluster is using x86_64-redhat-linux 4.1.2 GCC. I just did a quick yum search and there doesn't seem to be a newer GCC. We know you are going to cmake but we have yet to get it implemented on our cluster successfully. There have been doubts about the 4.1.x series of GCC compilers for GROMACS - and IIRC 4.1.2 in particular (do search the archives yourself). Some time back, Berk solicited actual accounts of problems and nobody presented one. So we no longer have an official warning against using
Re: [gmx-users] Two machines, same job, one fails
TJ Mustard wrote: snip 1. Do the systems in question crash immediately (i.e., step zero) or do they run for some time? Step 0, every time. 2. If they give you even a little bit of output, you can analyze which energy terms, etc go haywire with the tips listed here: All I have seen on these is LINCS Errors and Water molecules unable to be settled. But I will check this out right now, and email if I smell trouble. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System That would help in tracking down any potential bug or error. 3. Is it just the production runs that are crashing, or everything? If EM isn't even working, that smells even buggier. Awesome question here, we have seen some weird stuff. Sometimes the cluster will give us segmentation faults, then it will fail on our machines or sometimes not on our iMacs. I know weird! If EM starts on the cluster it will finish. Where we have issues is in positional restraint (PR) and MD and MD/FEP. It doesn't matter if FEP is on or off in a MD (although we are using SD for these MD/FEP runs). Does sometimes refer to different simulations, or multiple invocations of the same simulation system? If you're referencing the fact that system A works while system B doesn't, we're talking apples and oranges and it's irrelevant to the diagnosis (and perhaps some systems simply require greater finesse or a different protocol). If one system continually fails on one system and works on another, that's what we need to be discussing. Sorry if I've missed something, I'm just getting confused. 4. Are the compilers the same on the iMac vs. AMD cluster? No I am using x86_64-apple-darwin10 GCC 4.4.4 and the cluster is using x86_64-redhat-linux 4.1.2 GCC. Well, I know that for years weird behavior has been attributed to the gcc-4.1.x series, including the famous warning on the downloads page: WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distributions like Fedora 5/6 etc. I don't know if those issues were ever resolved (some error in Gromacs that wasn't playing nice with gcc, or vice versa). I just did a quick yum search and there doesn't seem to be a newer GCC. We know you are going to cmake but we have yet to get it implemented on our cluster successfully. The build system is irrelevant. You still need a reliable C compiler, whether using autoconf or cmake. -Justin Thank you, TJ Mustard -Justin Now I understand that my iMac works, but it only has 2 cpus and the cluster has 320. Since we are running our jobs via a Bennet's Acceptance Ratio FEP with 21 lambda windows, using just one 2 cpu machine would take too long. Especially since we wish to start pseudo high throughput drug testing. In my .mdp files now, the only changes are: (the default setting is on the right of the ;) define = ; = ; RUN CONTROL PARAMETERS integrator = sd; = md ; Start time and timestep in ps tinit= 0; = 0 dt = 0.004; = 0.001 nsteps = 75 ; = 0 (this one depends on the window and particular part of our job) ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1; = 100 (to save on disk space) nstvout = 1; = 100 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME; = Cutoff rcoulomb-switch = 0; = 0 rcoulomb = 1 ; = 1 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1; = 1 epsilon_rf = 1; = 1 ; Method for doing Van der Waals vdw-type = Cut-off; = Cut-off ; cut-off lengths rvdw-switch = 0; = 0 rvdw = 1 ; = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12; = 0.12 ; EWALD/PME/PPPM parameters pme_order= 4; = 4 ewald_rtol = 1e-05; = 1e-05 ewald_geometry = 3d; = 3d epsilon_surface = 0; = 0 optimize_fft = yes; = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = v-rescale; = No nsttcouple = -1; = -1 nh-chain-length = 10; = 10 ; Groups to couple separately tc-grps = System; = ; Time constant (ps) and reference temperature (K) tau-t= 0.1; = ref-t= 300; = ; Pressure coupling Pcoupl
Re: [gmx-users] (no subject)
trevor brown wrote: Dear Justin/Mark, I would like to have a private course about Gromacs in Holland. Is there such a facility for this? Who should I talk with? Can't help you there. I'm in the U.S. Or is there a workshop in near future? Any workshops will surely be announced on the list, but there haven't been any Gromacs-specific ones for several years. -Justin best wishes -- 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] Two machines, same job, one fails
On January 25, 2011 at 3:54 PM Mark Abraham mark.abra...@anu.edu.au wrote: On 01/26/11, TJ Mustard musta...@onid.orst.edu wrote: On January 25, 2011 at 3:24 PM Justin A. Lemkul jalem...@vt.edu wrote: TJ Mustard wrote: On January 25, 2011 at 2:08 PM Mark Abraham mark.abra...@anu.edu.au wrote: On 26/01/2011 5:50 AM, TJ Mustard wrote: Hi all, I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and FFTW 3.2.2. My iMac will run the job (over 4000 steps, till I killed it) at 4fs steps. (I am using heavy H) Once I put this on our groups AMD Cluster the jobs fail even with 2fs steps. (with thousands of lincs errors) We have recompiled the clusters gromacs 4.5.3 build, with no change. I know the system is the same since I copied the job from the server to my machine, to rerun it. What is going on? Why can one machine run a job perfectly and the other cannot? I also know there is adequate memory on both machines. Youve posted this before, and I made a number of diagnostic suggestions. What did you learn? Mark Mark and all, First thank you for all our help. What you suggested last time helped considerably with our jobs/calculations. I have learned that using the standard mdp settings allow my heavyh 4fs jobs to run on my iMac (intel) and have made these my new standard for future jobs. We chose to use the smaller 0.8nm PME/Cutoff due to others papers/tutorials, but now we understand why we need these standard settings. Now what I see to be our problem is that our machines have some sort of variable we cannot account for. If I am blind to my error, please show me. I just dont understand why one computer works while the other does not. We have recompiled gromacs 4.5.3 single precission on our cluster, and still have this problem. I know the feeling all too well. PowerPC jobs crash instantly, on our cluster, despite working beautifully on our lab machines. Theres a bug report about that one, but I havent heard anything about AMD failures. It remains a possibility that something beyond your control is going on. To explore a bit further: 1. Do the systems in question crash immediately (i.e., step zero) or do they run for some time? Step 0, every time. 2. If they give you even a little bit of output, you can analyze which energy terms, etc go haywire with the tips listed here: All I have seen on these is LINCS Errors and Water molecules unable to be settled. But I will check this out right now, and email if I smell trouble. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
Re: [gmx-users] Two machines, same job, one fails
On January 25, 2011 at 3:53 PM Justin A. Lemkul jalem...@vt.edu wrote: TJ Mustard wrote: snip 1. Do the systems in question crash immediately (i.e., step zero) or do they run for some time? Step 0, every time. 2. If they give you even a little bit of output, you can analyze which energy terms, etc go haywire with the tips listed here: All I have seen on these is LINCS Errors and Water molecules unable to be settled. But I will check this out right now, and email if I smell trouble. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System That would help in tracking down any potential bug or error. 3. Is it just the production runs that are crashing, or everything? If EM isnt even working, that smells even buggier. Awesome question here, we have seen some weird stuff. Sometimes the cluster will give us segmentation faults, then it will fail on our machines or sometimes not on our iMacs. I know weird! If EM starts on the cluster it will finish. Where we have issues is in positional restraint (PR) and MD and MD/FEP. It doesnt matter if FEP is on or off in a MD (although we are using SD for these MD/FEP runs). Does sometimes refer to different simulations, or multiple invocations of the same simulation system? If youre referencing the fact that system A works while system B doesnt, were talking apples and oranges and its irrelevant to the diagnosis (and perhaps some systems simply require greater finesse or a different protocol). If one system continually fails on one system and works on another, thats what we need to be discussing. Sorry if Ive missed something, Im just getting confused. What trends I see are that some jobs that segment fault on the cluster will also fault on our machines. But then when they fail on the cluster, via segmentation faults, they will work on our machines. Never does a single job sometimes fail and sometimes not, it either does or does not, every time. We have just gotten used to rebuilding our system and starting these again. We have also gotten used to doing EM on our machines and transferring this folder to be completed on the cluster. Once there it can finish the PR, MD and FEP. 4. Are the compilers the same on the iMac vs. AMD cluster? No I am using x86_64-apple-darwin10 GCC 4.4.4 and the cluster is using x86_64-redhat-linux 4.1.2 GCC. Well, I know that for years weird behavior has been attributed to the gcc-4.1.x series, including the famous warning on the downloads page: WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distributions like Fedora 5/6 etc. I dont know if those issues were ever resolved (some error in Gromacs that wasnt playing nice with gcc, or vice versa). Yes I am looking into this now. I hope this is our problem and not some hugely time consuming underlying problem with our system. Thank you. Thanks again, TJ Mustard I just did a quick yum search and there doesnt seem to be a newer GCC. We know you are going to cmake but we have yet to get it implemented on our cluster successfully. The build system is irrelevant. You still need a reliable C compiler, whether using autoconf or cmake. -Justin Thank you, TJ Mustard -Justin Now I understand that my iMac works, but it only has 2 cpus and the cluster has 320. Since we are running our jobs via a Bennets Acceptance Ratio FEP with 21 lambda windows, using just one 2 cpu machine would take too long. Especially since we wish to start pseudo high throughput drug testing. In my .mdp files now, the only changes are: (the default setting is on the right of the ;) define = ; = ; RUN CONTROL PARAMETERS integrator = sd ; = md ; Start time and timestep in ps tinit = 0 ; = 0 dt = 0.004 ; = 0.001 nsteps = 75 ; = 0 (this one depends on the window and particular part of our
[gmx-users] Fw:Re:gmx-users Digest, Vol 81, Issue 192; PME, Estimate for the relative
Hi Justin, .mdp and fourierspacing are at below, can you tell me where is not wrong? ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 300 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1 compressibility = 4.5e-5 ref_p= 1.0 ; Random seed for Andersen thermostat andersen_seed= 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing= no ; Number of time points to use for specifying annealing in each group annealing_npoints= ; List of times at the annealing points for each group annealing_time = ; Temp. at each annealing point, for each group. annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 gen_seed = 1993 Message: 4 Date: Tue, 25 Jan 2011 08:05:44 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relativecomputational load of the PME mesh part: 0.97 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d3ecaa8.60...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed gromacs wrote: HI Friends, I get the following note, The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. I want to keep the T at 300K, so does it matter to select any thermostat method? The choice of thermostat certainly does matter, otherwise you wouldn't get this note. Refer to the numerous discussions in the list archive as to why one would or would not (usually) use the Berendsen thermostat, as well as: http://www.gromacs.org/Documentation/Terminology/Thermostats http://www.gromacs.org/Documentation/Terminology/Berendsen Another note when i use PME: Estimate for the relative computational load of the PME mesh part: 0.97 NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing So what is the reason? I use type=PME Your combination of settings (rcoulomb, fourierspacing, and perhaps a few others) indicate that your simulation is going to spend an inordinate amount of time doing PME calculations, so your performance will suffer. Seeing your entire .mdp file would be necessary if you want further guidance. -Justin Is my setting proper? Thanks -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee
Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97
gromacs wrote: Hi Justin, .mdp and fourierspacing are at below, can you tell me where is not wrong? I see nothing wrong with the .mdp file, per se, although it does not appear complete (no integrator, nsteps, etc). Perhaps that was your intention, but if nsteps is left at default (0), then you shouldn't worry about poor performance :) The amount of time spent doing PME calculations depends on what is in your system. While your settings seems reasonable in a generic sense, if you have a large, highly-charged system, then much of the work will be allocated to PME. In that case, you may have to re-think how you balance the real space and reciprocal space terms. This involves possibly increasing (slightly) the values of rcoulomb and fourierspacing, if and only if the PME load is prohibitive and you are sure you won't incur any unnecessary error. g_pme_error may help there. -Justin ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.2 ; App ly long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol n bsp; = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc nbs p;= 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 300 ; Pressure coupling Pcoupl nbsp;= no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1 compressibility = 4.5e-5 ref_p= 1.0 ; Random seed for Andersen thermostat andersen_seed= 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing= no ; Number of time points to use for specify ing annealing in each group annealing_npoints= ; List of times at the annealing points for each group annealing_time = ; Temp. at each annealing point, for each group. annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 gen_seed = 1993 Message: 4 Date: Tue, 25 Jan 2011 08:05:44 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relativecomputational load of the PME mesh part: 0.97 To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4d3ecaa8.60...@vt.edu mailto:4d3ecaa8.60...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed gromacs wrote: HI Friends, I get the following note, The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. I want to keep the T at 300K, so does it matter to select any thermostat method? The choice of thermostat certainly does matter, otherwise you wouldn't get this note. Refer to the numerous discussions in the list archive as to why one would or would not (usually) use the Berendsen thermostat, as well as: http://www.gromacs.org/Documentation/Terminology/Thermostats
[gmx-users] More than one settle type
Hi, I am trying to find the free energy of a water molecule as it adsorbs on a surface. My outline is: 1) Run the simulation 2) Analyze the results, find out which water molecule(s) are adsorbed 3) Create different groups for the water adsordbed molecule(s), create new .gro file (to identify the adsorbed water with different residue name), .mdp file and .tpe file. The remaining water molecules have the same previous group name. 4) Use mdrun -rerun to evaluate the energy between the new water group(s), the surface and the remaining water. When I try to implement this, I get an error in step 4 while running mdrun -rerun, saying More than one settle type. Suggestion: change the least use settle constraints into 3 normal constraints. The .itp file which I created for the new water group is identical to the spc.itp file (with the only change as the residue name). This similar problem was raised earlier as well, which I am not sure if it was resolved: http://lists.gromacs.org/pipermail/gmx-users/2010-January/048058.html Basically, what I am trying to do is if I have 1000 water molecules in my system, can I have 999 of them in one group SOL, and the remaning 1 water molecule in a different group, say SOL1. The .itp files and parameters are identical, apart from the group (residue) name. And I am getting the above error. Anyone any ideas? Thanks in advance! -- 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] More than one settle type
On 01/26/11, Shalabh shal...@ufl.edu wrote: Hi, I am trying to find the free energy of a water molecule as it adsorbs on a surface. My outline is: 1) Run the simulation 2) Analyze the results, find out which water molecule(s) are adsorbed 3) Create different groups for the water adsordbed molecule(s), create new .gro file (to identify the adsorbed water with different residue name), .mdp file and .tpe file. The remaining water molecules have the same previous group name. You're making life hard for yourself by renaming the residue, which you don't need to do. You merely need to divide the solvent into two groups for energy evaluation, and you can do that with a suitably constructed index file and matching .mdp as grompp input. If you use g_select with a suitable geometric criterion for adsorbation, then it can write the index file for you (and there are various ways you might visualise the result to check it). All you need to do is decide on the criterion, name the groups, modify the .mdp and feed it to grompp. 4) Use mdrun -rerun to evaluate the energy between the new water group(s), the surface and the remaining water. When I try to implement this, I get an error in step 4 while running mdrun -rerun, saying More than one settle type. Suggestion: change the least use settle constraints into 3 normal constraints. The .itp file which I created for the new water group is identical to the spc.itp file (with the only change as the residue name). This similar problem was raised earlier as well, which I am not sure if it was resolved: http://lists.gromacs.org/pipermail/gmx-users/2010-January/048058.html Basically, what I am trying to do is if I have 1000 water molecules in my system, can I have 999 of them in one group SOL, and the remaning 1 water molecule in a different group, say SOL1. The .itp files and parameters are identical, apart from the group (residue) name. And I am getting the above error. Anyone any ideas? Groups and molecule blocks in the topology need not relate to each other at all. It is simplest to leave your .top file alone and follow the approach I suggested above. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] QMMM with ORCA
Hi, All, I'm trying to see if anybody has experience of using the interface of gromacs and ORCA(since it's free). I know that the following link gave information on how http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code But.But, the gromacs in the above link is quite old(3.2). I download the latest 4.5.3 and followed the instructions in the above link and I was trying to optimize an simple cluster(no pbc) where part of it are treated using QM. here is the example mdp file = title = cpeptide integrator = steep ;integrator includes energy minimization algorithms dt = 0.002; ps ! nsteps = 1 nstlist = 1 ns_type = simple rlist = 3.0 rcoulomb= 3.0 coulombtype = cut-off vdwtype = cut-off rvdw= 3.0 pbc = no periodic_molecules = no constraints = none energygrps = qm_part mm_part ; QM/MM calculation stuff QMMM = yes QMMM-grps = qm_part QMmethod = rhf QMbasis = 3-21G QMMMscheme = oniom QMcharge = 0 QMmult = 1 ; ; Energy minimizing stuff ; emtol = 60 ; minimization thresold (kj/mol.nm-1)1 hartree/bohr= 49614.75241 kj/mol.nm-1 1 kj/mol.nm-1=2.01553e-5 hartree/bohr emstep = 0.01 ; minimization step in nm = I set up the BASENAME and ORCA_PATH as told in the instruction. first of all, the normal electronic embedding just simply gave segmentation fault error right after the it prints information on number of steps of optimization. So I switch to ONIOM, this time, at least, orca is called and energy and gradient are both generated. However, when it comes to read the energy and gradient, it always crashes when tried to read gradient, this is at *line 346* source code src/mdlib/qm_orca.c sscanf(buf,%lf\n, QMgrad[k][XX]); a segmentation fault error is printed. If I replace the QMgrad[k][XX] by an temporary variable temp sscanf(buf,%lf\n, temp); temp gets the correct value and if I use, QMgrad[k][XX]=temp and tries to print QMgrad[k][XX], a bus error will be printed. I did some research online, seems that usually this implies an memory bug in the code which is the most difficult bug one can ever encounter. So has anyone successfully used gromacs and orca to do QMMM? Generally, would anyone recommend using gromacs to do QMMM? Cheers, Xiaohu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: stopping a simulation in between without crashing any trajectories
Hi, I ran a simulation of 10ns and now it has completed till 5ns .. I want to stop it now and retrieve the trajectories without any errors.. Is it possible to do that ?? -- Bharat -- 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
