Re: [gmx-users] Re grompp and mdrun output files

2014-07-25 Thread Giuseppina La Sala
Hi Melsa, I think that your problem could belong to the fact that in the .xtc file you do not write all the frames, but every n-steps. Thus, the last frame of your xtc file is a multiple of n-step (a discrete value) and not necessary the real last one, that for sure is represented by md300.gro.

[gmx-users] g_cluster analysis for structure refirement

2014-07-25 Thread James Starlight
Dear Gromacs users! I'd like to use g_cluster utility to cluster a big set of models produced by Modeller as the result of the refirement of some parts of my protein. In this case all structures differs only in the conformation of 1 longest loop (~ 30 amino acids including 2 disulphide bridges)

Re: [gmx-users] g_cluster analysis for structure refirement

2014-07-25 Thread Tsjerk Wassenaar
Hi James, The first part is just conformational clustering, for which you can use g_cluster. The easiest is then to collect the structures belonging to the different clusters in different files (which g_cluster can do), which you process separately to extract those properties you're interested

Re: [gmx-users] Gromacs performance on virtual servers

2014-07-25 Thread Mark Abraham
On Fri, Jul 25, 2014 at 1:51 AM, Szilárd Páll pall.szil...@gmail.com wrote: Hi In general, virtualization will always have an overhead, but if done well, the performance should be close to that of bare metal. However, for GROMACS the ideal scenario is exclusive host access (including

[gmx-users] Groups in index.ndx

2014-07-25 Thread INPE (Ingrid Viveka Pettersson)
Dear Group, I have defined different specific groups in the index.ndx file. My problem is that if I try to add a new group, the old ones are disappearing. Should it be like this? Yours sincerely, Ingrid Pettersson _ Ingrid Pettersson, PhD Principal Scientist

Re: [gmx-users] Angle group

2014-07-25 Thread Justin Lemkul
On 7/25/14, 7:35 AM, Cyrus Djahedi wrote: There is something else. I also tried using mk_angndx to generate an index file prior to using g_angle by: mk_angndx -s C0.tpr -type angle It generates a lot of different angle group that I can not identify. Each line in the index-file has 9 atoms in

[gmx-users] hints for core/shell optimization?

2014-07-25 Thread Tamas Karpati
Dear all, I have two questions about geometry optimization of a crystal with polarization via the core/shell model. I'm creating *.gro and *.top files by hand and compile them with *.mdp to *.tpr via GROMPP. My FF is also made by hand (simply because i need to learn GROMACS). I have learnt on

[gmx-users] Lennard jones parameters for metal ions

2014-07-25 Thread #SUKRITI GUPTA#
Dear Gromacs users, I wanted to simulate metal ions in gromacs. For Fe+2, I have lj potential parameters already defined in OPLSAA forcefield, so I wanted to know if I want to add FE+3 in my simulation, then the LJ parameters for it will be different from that of Fe+2 or same? I thought it

Re: [gmx-users] Lennard jones parameters for ions

2014-07-25 Thread Justin Lemkul
On 7/25/14, 7:39 AM, #SUKRITI GUPTA# wrote: Dear Gromacs users, I wanted to simulate metal ions in gromacs. For Fe+2, I have lj potential parameters already defined in OPLSAA forcefield, so I wanted to know if I want to add FE+3 in my simulation, then the LJ parameters for it will be

Re: [gmx-users] hints for core/shell optimization?

2014-07-25 Thread Justin Lemkul
On 7/25/14, 7:43 AM, Tamas Karpati wrote: Dear all, I have two questions about geometry optimization of a crystal with polarization via the core/shell model. I'm creating *.gro and *.top files by hand and compile them with *.mdp to *.tpr via GROMPP. My FF is also made by hand (simply because

Re: [gmx-users] Groups in index.ndx

2014-07-25 Thread INPE (Ingrid Viveka Pettersson)
Thank you for the help. It works fine. BR Ingrid -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: 25. juli 2014 13:36 To: gmx-us...@gromacs.org Subject: Re:

[gmx-users] Lennard jones parameters for ions

2014-07-25 Thread #SUKRITI GUPTA#
Dear Gromacs users, I wanted to simulate metal ions in gromacs. For Fe+2, I have lj potential parameters already defined in OPLSAA forcefield, so I wanted to know if I want to add FE+3 in my simulation, then the LJ parameters for it will be different from that of Fe+2 or same? I thought it

Re: [gmx-users] Groups in index.ndx

2014-07-25 Thread Nidhi Katyal
Use make_ndx -f *.gro -n old_index.ndx -o old_index.ndx On Fri, Jul 25, 2014 at 4:53 PM, INPE (Ingrid Viveka Pettersson) i...@novonordisk.com wrote: Dear Group, I have defined different specific groups in the index.ndx file. My problem is that if I try to add a new group, the old ones are

Re: [gmx-users] hints for core/shell optimization?

2014-07-25 Thread Tamas Karpati
Dear Justin, Thank you for your quick answer. Same with GROMACS-4.6.6: core-to-shell distance must be 0 to not crash. My crystal is expected to be polarized (metallic and oxygen sites are the victims of this model). The *.mpd file being used is: # nstcalcenergy = 1 ; 4.6.6 claims this

Re: [gmx-users] Lennard jones parameters for ions

2014-07-25 Thread #SUKRITI GUPTA#
Dear Justin, Thanks for your reply. Then it there any relation between charge density (for same element) and lj parameters e.g. for higher charge vander waals radius is smaller? Or are lj parameters randomly selected just to satisfy physical behavior of the ions? Regards Sukriti Sukriti

Re: [gmx-users] Lennard jones parameters for ions

2014-07-25 Thread Justin Lemkul
On 7/25/14, 8:21 AM, #SUKRITI GUPTA# wrote: Dear Justin, Thanks for your reply. Then it there any relation between charge density (for same element) and lj parameters e.g. for higher charge vander waals radius is smaller? Or are lj parameters randomly selected just to satisfy physical

Re: [gmx-users] hints for core/shell optimization?

2014-07-25 Thread Justin Lemkul
On 7/25/14, 8:10 AM, Tamas Karpati wrote: Dear Justin, Thank you for your quick answer. Same with GROMACS-4.6.6: core-to-shell distance must be 0 to not crash. My crystal is expected to be polarized Does your topology specify the proper intramolecular exclusions? What is(are) the

[gmx-users] genbox_mpi and Error: Invalid number of threads defined

2014-07-25 Thread lswierczewski .
Dear GROMACS Users, I have a problem when running genbox_mpi. Below is information from the console. [lswiercz@nostromo ~/gromacs]$ srun --nodes 1 genbox_mpi -cp 1AKI_newbox.gro -cs spc216.gro -p topol.top -o solvated.gro srun: job 5026 queued and waiting for resources srun: job 5026 has been

Re: [gmx-users] genbox_mpi and Error: Invalid number of threads defined

2014-07-25 Thread Justin Lemkul
On 7/25/14, 11:20 AM, lswierczewski . wrote: Dear GROMACS Users, I have a problem when running genbox_mpi. Below is information from the console. [lswiercz@nostromo ~/gromacs]$ srun --nodes 1 genbox_mpi -cp 1AKI_newbox.gro -cs spc216.gro -p topol.top -o solvated.gro srun: job 5026 queued

Re: [gmx-users] hints for core/shell optimization?

2014-07-25 Thread Justin Lemkul
On 7/25/14, 11:22 AM, Tamas Karpati wrote: Dear Justin, Does your topology specify the proper intramolecular exclusions? What is(are) the molecule(s)? No bonds, no exclusions. The whole crystal is modelled by ions interacting via forces of the Coulomb and Buckingham types. In fact, there

Re: [gmx-users] hints for core/shell optimization?

2014-07-25 Thread Tamas Karpati
Dear Justin, Does your topology specify the proper intramolecular exclusions? What is(are) the molecule(s)? No bonds, no exclusions. The whole crystal is modelled by ions interacting via forces of the Coulomb and Buckingham types. In fact, there is an X-Y-X angle force type which does have an

Re: [gmx-users] hints for core/shell optimization?

2014-07-25 Thread Tamas Karpati
Dear Justin, Thanks for your educational answers. Coulombic interactions fail at short distances; you probably need to apply I was afraid of that... somehow removing shells from the cores in the initial structure have let it functionally work (with not yet reasonable results). Thole

Re: [gmx-users] Gromacs performance on virtual servers

2014-07-25 Thread Szilárd Páll
On Fri, Jul 25, 2014 at 12:33 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Fri, Jul 25, 2014 at 1:51 AM, Szilárd Páll pall.szil...@gmail.com wrote: Hi In general, virtualization will always have an overhead, but if done well, the performance should be close to that of bare metal.

Re: [gmx-users] time accounting in log file with GPU

2014-07-25 Thread Mark Abraham
They report the time since the step that the timers were reset. The log file will note this event. Whether load is balanced by then/ever depends on the load. Mark On Jul 25, 2014 7:31 PM, Sikandar Mashayak symasha...@gmail.com wrote: Thanks Szilárd. I am bit confused about the -resethway or

Re: [gmx-users] time accounting in log file with GPU

2014-07-25 Thread Sikandar Mashayak
Got it! Thanks Mark. On Fri, Jul 25, 2014 at 10:41 AM, Mark Abraham mark.j.abra...@gmail.com wrote: They report the time since the step that the timers were reset. The log file will note this event. Whether load is balanced by then/ever depends on the load. Mark On Jul 25, 2014 7:31 PM,

Re: [gmx-users] hints for core/shell optimization?

2014-07-25 Thread Justin Lemkul
On 7/25/14, 12:40 PM, Tamas Karpati wrote: Dear Justin, Thanks for your educational answers. Coulombic interactions fail at short distances; you probably need to apply I was afraid of that... somehow removing shells from the cores in the initial structure have let it functionally work

Re: [gmx-users] Can't run v. 4.6.6 on worker nodes if they are compiled with SIMD

2014-07-25 Thread Justin Lemkul
On 7/25/14, 4:17 PM, Seyyed Mohtadin Hashemi wrote: On Fri, Jul 25, 2014 at 3:00 PM, Seyyed Mohtadin Hashemi haa...@gmail.com wrote: Hi everyone, I'm having a very weird problem with GROMACS 4.6.6: I am currently testing out GPU capabilities and was trying to compile GROMACS with CUDA

Re: [gmx-users] Can't run v. 4.6.6 on worker nodes if they are compiled with SIMD

2014-07-25 Thread Seyyed Mohtadin Hashemi
On Fri, Jul 25, 2014 at 3:17 PM, Seyyed Mohtadin Hashemi haa...@gmail.com wrote: On Fri, Jul 25, 2014 at 3:00 PM, Seyyed Mohtadin Hashemi haa...@gmail.com wrote: Hi everyone, I'm having a very weird problem with GROMACS 4.6.6: I am currently testing out GPU capabilities and was trying to

[gmx-users] electrostatics forces and van der waals forces calculation

2014-07-25 Thread Andy Chao
Dear GROMACS Users: Would you please let me know how to calculate/extract the electrostatic forces and van der waals forces of an ionic liquid structure in GROMACS? Which GROMACS command should I use? g_enemat? g_potential? Thanks a lot! Andy -- Gromacs Users mailing list * Please search