Re: [gmx-users] Re grompp and mdrun output files
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. Cheers Josephine Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] per conto di Melsa Rose Ducut [ducut_melsar...@yahoo.com] Inviato: venerdì 25 luglio 2014 6.50 A: gromacs.org_gmx-users@maillist.sys.kth.se Oggetto: [gmx-users] Re grompp and mdrun output files Hi GROMACS users, I typed the command grompp -f md300.mdp -c equi_new.gro -n dex.ndx -p topol.top -maxwarn 1 -o md300.tpr then this command mdrun -v -deffnm md300 So, I was expecting that the md300.gro output file will be same to the last frame when I load the md300.xtc on the equi_new.gro file on vmd. However, that is not the case. Can anyone please enlighten me about this? Thanks. regards, Melsa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_cluster analysis for structure refirement
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) so I need to cluster all models based on the RMSD in this region. As the result I'd like to obtain projection of all set of conformers onto the plane of some coordinates correspond to some selected structural criteriums (for instance percent of the occurence of secondary structure elements in the refined (loop) region; and/or some geometrical criteriums like distance between pair of residues, occurence of the salt-bridges in this region etc. As the result I'd like to visualize data and chose most representative structures from each cluster for further MD simulation. Could such processing be performed by g_cluster taking into account that I have gromacs-like trr consisted of my conformers ? On what cluster algoritms and parameters should I pay a lot of attention? Many thanks for suggestion, James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_cluster analysis for structure refirement
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 in. Then you can easily plot the selected properties per cluster. Hope it helps, Tsjerk On Fri, Jul 25, 2014 at 9:53 AM, James Starlight jmsstarli...@gmail.com wrote: 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) so I need to cluster all models based on the RMSD in this region. As the result I'd like to obtain projection of all set of conformers onto the plane of some coordinates correspond to some selected structural criteriums (for instance percent of the occurence of secondary structure elements in the refined (loop) region; and/or some geometrical criteriums like distance between pair of residues, occurence of the salt-bridges in this region etc. As the result I'd like to visualize data and chose most representative structures from each cluster for further MD simulation. Could such processing be performed by g_cluster taking into account that I have gromacs-like trr consisted of my conformers ? On what cluster algoritms and parameters should I pay a lot of attention? Many thanks for suggestion, James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs performance on virtual servers
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 hypervisor) and thread affinities which will both depend on the hypervisor configuration. Hence, if you can, you should try to get access to virtual hosts that fully utilize a compute node and do not share it with others. Definitely. On Fri, Jul 25, 2014 at 12:31 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Except for huge simulation systems, GROMACS performance past a single node is dominated by network latency, so unless you can extract a promise that any multi-node runs will have Infiniband-quality latency (because the nodes are physically in the same room, and on Infiniband) you can forget about doing multi-node MD on such a system. Two remarks: * With a slow network the only parallelization you can potentially make use of is multi-sim, unless your environment is so could-y that some nodes can have tens to hundreds of ms latency which can kill even you multi-sim performance (depending on how fast each simulation is and how often do they sync). I would not encourage multi-sim on such a setup, unless you actually want replica exchange. The multi-sim implementation unnecessarily syncs simulations every min(nstlist,nstcalcenergy,nstreplex) step, so that might be ~tens of times per second. Unnecessary multi-sim is good for pretending you are doing a big parallel calculation to get access to a large chunk of a machine, but this is not really the case here. * I've seen several claims that *good* 10/40G Ethernet can get close to IB even in latency, even for MD, and even for GROMACS, e.g: http://goo.gl/JrNxKf, http://goo.gl/t0z15f Interesting, thanks. Mark Cheers, -- Szilárd Mark On Thu, Jul 24, 2014 at 10:54 PM, Elton Carvalho elto...@if.usp.br wrote: Dear Gromacs Users, My former university is focusing on cloud computing instead of physical servers, so research groups are now expected to buy virtual servers from the university coloud instead of buying their own clusters. The current setup employs Xeon E7- 2870 servers and there is an university-wide virtual cluster with 50 virtual servers each with 10 CPUs. Does anyone here have information on gromacs performance on this kind of infrastructure? Should I expect big issues? One thing that comes to mind is that the CPUs may not necessarily be in the same physical server, rack, or even datacenter (their plan is to decentralize the colocation), so network latency may be higher than the traditional setup, which may affect scaling. Does this argument make sense or am I missing something on cloud management 101? Cheers. -- Elton Carvalho Departamento de Física Universidade Federal do Paraná -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Groups in index.ndx
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 Diabetes Structural Biology Novo Nordisk A/S Novo Nordisk Park DK-2760 Måløv Denmark +4530754506 (direct) i...@novonordisk.com Facebookhttp://www.facebook.com/novonordisk | Twitterhttp://www.twitter.com/novonordisk | LinkedInhttp://www.linkedin.com/company/novo-nordisk | Youtubehttp://www.Youtube.com/novonordisk | Pinteresthttp://www.pinterest.com/novonordisk This e-mail (including any attachments) is intended for the addressee(s) stated above only and may contain confidential information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information contained herein is strictly prohibited and may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete it immediately hereafter. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Angle group
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 it, are the atoms divided three-by-three to form a triplet? Is there any way of knowing which group represents which triplet? g_angle: Group 0 (Theta=110.0_502.42) has 7680 elements Group 1 (Theta=111.0_376.81) has 10560 elements Group 2 (Theta=112.0_837.36) has 960 elements Group 3 (Theta=107.5_586.15) has 4944 elements Group 4 (Theta=108.5_586.15) has 5616 elements Group 5 (Theta=109.5_460.55) has 2976 elements Group 6 (Theta=113.5_376.81) has 3840 elements Group 7 (Theta=111.6_418.68) has 1872 elements Group 8 (Theta=109.5_376.81) has 960 elements Select a group: 2 Selected 2: 'Theta=112.0_837.36' Last frame 1 time 1.000 Found points in the range from 93 to 124 (max 180) angle = 108.363 angle^2 = 11742.5 Std. Dev. = 0.214073 mk_angndx divides the groups based on their parameters, not necessarily by the same chemical definition (i.e. the same bonded parameters may apply to different groups in your structure). You can always identify what the groups contain by opening the .ndx file in a text editor; all an .ndx file has is a list of atom numbers, so it's easy to tell what is what. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] hints for core/shell optimization?
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 this list that with Buckingham potentials I need to use the group rather than the Verlet scheme. (1/2) Letting some of all atoms be polarizable through applying shell particles made MDRUN segfault like this: # ... # Reading file AAA_opt.tpr, VERSION 4.6.3 (single precision) # Using 2 MPI threads # # Steepest Descents: # Tolerance (Fmax) = 1.0e+01 #Number of steps= 10 # Segmentation fault1.0e-02 nm, Epot= -nan Fmax= 3.76506e+03, atom= 1357 I imagined some divison by zero situation not handled and have put some random noise on the shell particles' position so they do not anymore start exactly at the atomic sites (meaning nonzero distances). Seemed to work, at least no further crashes. Only energies and forces seem very high: # Steepest Descents: # Tolerance (Fmax) = 1.0e+01 # Number of steps= 10 # Step=0, Dmax= 1.0e-02 nm, Epot= -1.36425e+07 Fmax= 2.99600e+05, atom= 160 # Step=1, Dmax= 1.0e-02 nm, Epot= -1.62080e+07 Fmax= 1.25769e+06, atom= 160 # Step=2, Dmax= 1.2e-02 nm, Epot= -1.95965e+07 Fmax= 6.87820e+08, atom= 2759 # Step=3, Dmax= 1.4e-02 nm, Epot= -2.02902e+07 Fmax= 1.30719e+09, atom= 468 # Step=8, Dmax= 1.1e-03 nm, Epot= -2.18970e+07 Fmax= 5.77722e+09, atom= 1095 # Step= 10, Dmax= 6.5e-04 nm, Epot= -1.96952e+07 Fmax= 3.92889e+08, atom= 1096 # Energy minimization reached the maximum numberof steps before the forces # reached the requestedprecision Fmax 10. My question is the following. Is it (randomized shell positions) a correct procedure with GROMACS? (2/2) Changing from a randomized x/y/z set to a fixed distance at a random direction for the shell particles led to another unexpected result. I scanned a range between 1e-4 to 0.1 nm and noticed that the final core-to-shell distance is a function of the starting one. I used niter = 1 (note: the default is 20) as i noticed in an MD type of job that 20, 100 or 1000 steps were insufficient for the shells to relax within default tolerance. The cell size was ca. 3x3x3 nm. My question is the following. What would be the appropriate core-to-shell distance to apply? I appreciate any help so thanks in advance. With regards, toma -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Lennard jones parameters for metal ions
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 will be same because vander waals radii is defined for a element and not ion, hence it will be same for Fe or Fe+2 or Fe+3. Regards Sukriti [https://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sghttp://www.ntu.edu.sg/home/xuzc/People.html -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Lennard jones parameters for ions
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 different from that of Fe+2 or same? I thought it will be same because vander waals radii is defined for a element and not ion, hence it will be same for Fe or Fe+2 or Fe+3. In any force field, LJ and electrostatic terms are parametrized to balance in some way that produces some physically sensible behavior. Given the extremely high charge density of Fe2+ and Fe3+, I see no reason to think that the LJ parameters for one would be the same as for the other. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] hints for core/shell optimization?
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 i need to learn GROMACS). I have learnt on this list that with Buckingham potentials I need to use the group rather than the Verlet scheme. (1/2) Letting some of all atoms be polarizable through applying shell particles made MDRUN segfault like this: # ... # Reading file AAA_opt.tpr, VERSION 4.6.3 (single precision) # Using 2 MPI threads # # Steepest Descents: # Tolerance (Fmax) = 1.0e+01 #Number of steps= 10 # Segmentation fault1.0e-02 nm, Epot= -nan Fmax= 3.76506e+03, atom= 1357 I imagined some divison by zero situation not handled and have put some random noise on the shell particles' position so they do not anymore start exactly at the atomic sites (meaning nonzero distances). Seemed to work, at least no further crashes. Only energies and forces seem very high: # Steepest Descents: # Tolerance (Fmax) = 1.0e+01 # Number of steps= 10 # Step=0, Dmax= 1.0e-02 nm, Epot= -1.36425e+07 Fmax= 2.99600e+05, atom= 160 # Step=1, Dmax= 1.0e-02 nm, Epot= -1.62080e+07 Fmax= 1.25769e+06, atom= 160 # Step=2, Dmax= 1.2e-02 nm, Epot= -1.95965e+07 Fmax= 6.87820e+08, atom= 2759 # Step=3, Dmax= 1.4e-02 nm, Epot= -2.02902e+07 Fmax= 1.30719e+09, atom= 468 # Step=8, Dmax= 1.1e-03 nm, Epot= -2.18970e+07 Fmax= 5.77722e+09, atom= 1095 # Step= 10, Dmax= 6.5e-04 nm, Epot= -1.96952e+07 Fmax= 3.92889e+08, atom= 1096 # Energy minimization reached the maximum numberof steps before the forces # reached the requestedprecision Fmax 10. My question is the following. Is it (randomized shell positions) a correct procedure with GROMACS? (2/2) Changing from a randomized x/y/z set to a fixed distance at a random direction for the shell particles led to another unexpected result. I scanned a range between 1e-4 to 0.1 nm and noticed that the final core-to-shell distance is a function of the starting one. I used niter = 1 (note: the default is 20) as i noticed in an MD type of job that 20, 100 or 1000 steps were insufficient for the shells to relax within default tolerance. The cell size was ca. 3x3x3 nm. Please provide a full .mdp file; other settings are very relevant. My question is the following. What would be the appropriate core-to-shell distance to apply? The equilibrium distance for core-shell bonds should be zero, deviations from this non-polarized state account for the polarization energy. I appreciate any help so thanks in advance. Upgrade to 4.6.6; there have been issues with shells that have been fixed since 4.6.3. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Groups in index.ndx
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] Groups in index.ndx On 7/25/14, 7:23 AM, INPE (Ingrid Viveka Pettersson) 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 disappearing. Should it be like this? Depends on the way you're issuing make_ndx. You can preserve the existing custom groups when writing a new index file by supplying the old index file as input to make_ndx. If you're using default file names (hint: always provide your exact command!) then it will otherwise be overwritten. make_ndx -f conf.gro -n old_index.ndx -o new_index.ndx will preserve your custom groups and allow you to add new ones. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Lennard jones parameters for ions
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 will be same because vander waals radii is defined for a element and not ion, hence it will be same for Fe or Fe+2 or Fe+3. Regards Sukriti [https://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sghttp://www.ntu.edu.sg/home/xuzc/People.html -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Groups in index.ndx
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 disappearing. Should it be like this? Yours sincerely, Ingrid Pettersson _ Ingrid Pettersson, PhD Principal Scientist Diabetes Structural Biology Novo Nordisk A/S Novo Nordisk Park DK-2760 Måløv Denmark +4530754506 (direct) i...@novonordisk.com Facebookhttp://www.facebook.com/novonordisk | Twitter http://www.twitter.com/novonordisk | LinkedIn http://www.linkedin.com/company/novo-nordisk | Youtube http://www.Youtube.com/novonordisk | Pinterest http://www.pinterest.com/novonordisk This e-mail (including any attachments) is intended for the addressee(s) stated above only and may contain confidential information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information contained herein is strictly prohibited and may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete it immediately hereafter. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] hints for core/shell optimization?
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 necessary, 4.6.3 didn't need it # integrator = steep # vdw-type= cut-off # coulombtype = pme # nsteps = 10 # periodic-molecules = no # cutoff-scheme = group # ns-type = grid # emtol = 10 ; default=10 kJ/mol/nm # niter = 1 ; default=20 # ;fcstep = ; default=0 ps^2 ; not quite clear what it is # rlist = 1.0 # rcoulomb= 1.0 # rvdw= 1.0 # pbc = xyz # nstxout = 1 ; wouldn't emit pos for each, though # nstfout = 1 ; -- # nstlist = 1000 ; avoid it, no bonds at all # nstlog = 1 # ;pcoupl = no ; used to switch cell-optimization on/off Best regards, toma On Fri, Jul 25, 2014 at 1:48 PM, Justin Lemkul jalem...@vt.edu wrote: 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 i need to learn GROMACS). I have learnt on this list that with Buckingham potentials I need to use the group rather than the Verlet scheme. (1/2) Letting some of all atoms be polarizable through applying shell particles made MDRUN segfault like this: # ... # Reading file AAA_opt.tpr, VERSION 4.6.3 (single precision) # Using 2 MPI threads # # Steepest Descents: # Tolerance (Fmax) = 1.0e+01 #Number of steps= 10 # Segmentation fault1.0e-02 nm, Epot= -nan Fmax= 3.76506e+03, atom= 1357 I imagined some divison by zero situation not handled and have put some random noise on the shell particles' position so they do not anymore start exactly at the atomic sites (meaning nonzero distances). Seemed to work, at least no further crashes. Only energies and forces seem very high: # Steepest Descents: # Tolerance (Fmax) = 1.0e+01 # Number of steps= 10 # Step=0, Dmax= 1.0e-02 nm, Epot= -1.36425e+07 Fmax= 2.99600e+05, atom= 160 # Step=1, Dmax= 1.0e-02 nm, Epot= -1.62080e+07 Fmax= 1.25769e+06, atom= 160 # Step=2, Dmax= 1.2e-02 nm, Epot= -1.95965e+07 Fmax= 6.87820e+08, atom= 2759 # Step=3, Dmax= 1.4e-02 nm, Epot= -2.02902e+07 Fmax= 1.30719e+09, atom= 468 # Step=8, Dmax= 1.1e-03 nm, Epot= -2.18970e+07 Fmax= 5.77722e+09, atom= 1095 # Step= 10, Dmax= 6.5e-04 nm, Epot= -1.96952e+07 Fmax= 3.92889e+08, atom= 1096 # Energy minimization reached the maximum numberof steps before the forces # reached the requestedprecision Fmax 10. My question is the following. Is it (randomized shell positions) a correct procedure with GROMACS? (2/2) Changing from a randomized x/y/z set to a fixed distance at a random direction for the shell particles led to another unexpected result. I scanned a range between 1e-4 to 0.1 nm and noticed that the final core-to-shell distance is a function of the starting one. I used niter = 1 (note: the default is 20) as i noticed in an MD type of job that 20, 100 or 1000 steps were insufficient for the shells to relax within default tolerance. The cell size was ca. 3x3x3 nm. Please provide a full .mdp file; other settings are very relevant. My question is the following. What would be the appropriate core-to-shell distance to apply? The equilibrium distance for core-shell bonds should be zero, deviations from this non-polarized state account for the polarization energy. I appreciate any help so thanks in advance. Upgrade to 4.6.6; there have been issues with shells that have been fixed since 4.6.3. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe
Re: [gmx-users] Lennard jones parameters for ions
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 Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Friday, July 25, 2014 7:46 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Lennard jones parameters for ions 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 different from that of Fe+2 or same? I thought it will be same because vander waals radii is defined for a element and not ion, hence it will be same for Fe or Fe+2 or Fe+3. In any force field, LJ and electrostatic terms are parametrized to balance in some way that produces some physically sensible behavior. Given the extremely high charge density of Fe2+ and Fe3+, I see no reason to think that the LJ parameters for one would be the same as for the other. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Lennard jones parameters for ions
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 behavior of the ions? There's nothing random about it. You need some sort of target data - QM interaction energies, crystal geometries, hydration free energies, etc. to parametrize the model. The parameters are tuned to agree with whatever data are deemed suitable. Additive models of transition metals are generally very poor, though. There are many effects that simply can't be captured by a point charge with a 12-6 LJ potential. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] hints for core/shell optimization?
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 molecule(s)? (metallic and oxygen sites are the victims of this model). The *.mpd file being used is: # nstcalcenergy = 1 ; 4.6.6 claims this necessary, 4.6.3 didn't need it Definitely true. # integrator = steep # vdw-type= cut-off # coulombtype = pme # nsteps = 10 # periodic-molecules = no # cutoff-scheme = group # ns-type = grid # emtol = 10 ; default=10 kJ/mol/nm # niter = 1 ; default=20 # ;fcstep = ; default=0 ps^2 ; not quite clear what it is # rlist = 1.0 # rcoulomb= 1.0 # rvdw= 1.0 # pbc = xyz # nstxout = 1 ; wouldn't emit pos for each, though # nstfout = 1 ; -- # nstlist = 1000 ; avoid it, no bonds at all Try nstlist = 1. The shell positions are solved via SCF (EM), so you need to update the neighbor list very frequently. -Justin # nstlog = 1 # ;pcoupl = no ; used to switch cell-optimization on/off Best regards, toma On Fri, Jul 25, 2014 at 1:48 PM, Justin Lemkul jalem...@vt.edu wrote: 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 i need to learn GROMACS). I have learnt on this list that with Buckingham potentials I need to use the group rather than the Verlet scheme. (1/2) Letting some of all atoms be polarizable through applying shell particles made MDRUN segfault like this: # ... # Reading file AAA_opt.tpr, VERSION 4.6.3 (single precision) # Using 2 MPI threads # # Steepest Descents: # Tolerance (Fmax) = 1.0e+01 #Number of steps= 10 # Segmentation fault1.0e-02 nm, Epot= -nan Fmax= 3.76506e+03, atom= 1357 I imagined some divison by zero situation not handled and have put some random noise on the shell particles' position so they do not anymore start exactly at the atomic sites (meaning nonzero distances). Seemed to work, at least no further crashes. Only energies and forces seem very high: # Steepest Descents: # Tolerance (Fmax) = 1.0e+01 # Number of steps= 10 # Step=0, Dmax= 1.0e-02 nm, Epot= -1.36425e+07 Fmax= 2.99600e+05, atom= 160 # Step=1, Dmax= 1.0e-02 nm, Epot= -1.62080e+07 Fmax= 1.25769e+06, atom= 160 # Step=2, Dmax= 1.2e-02 nm, Epot= -1.95965e+07 Fmax= 6.87820e+08, atom= 2759 # Step=3, Dmax= 1.4e-02 nm, Epot= -2.02902e+07 Fmax= 1.30719e+09, atom= 468 # Step=8, Dmax= 1.1e-03 nm, Epot= -2.18970e+07 Fmax= 5.77722e+09, atom= 1095 # Step= 10, Dmax= 6.5e-04 nm, Epot= -1.96952e+07 Fmax= 3.92889e+08, atom= 1096 # Energy minimization reached the maximum numberof steps before the forces # reached the requestedprecision Fmax 10. My question is the following. Is it (randomized shell positions) a correct procedure with GROMACS? (2/2) Changing from a randomized x/y/z set to a fixed distance at a random direction for the shell particles led to another unexpected result. I scanned a range between 1e-4 to 0.1 nm and noticed that the final core-to-shell distance is a function of the starting one. I used niter = 1 (note: the default is 20) as i noticed in an MD type of job that 20, 100 or 1000 steps were insufficient for the shells to relax within default tolerance. The cell size was ca. 3x3x3 nm. Please provide a full .mdp file; other settings are very relevant. My question is the following. What would be the appropriate core-to-shell distance to apply? The equilibrium distance for core-shell bonds should be zero, deviations from this non-polarized state account for the polarization energy. I appreciate any help so thanks in advance. Upgrade to 4.6.6; there have been issues with shells that have been fixed since 4.6.3. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to
[gmx-users] genbox_mpi and Error: Invalid number of threads defined
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 allocated resources :-) G R O M A C S (-: Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) /opt/gromacs/4.6.3/bin/genbox_mpi (-: Option Filename Type Description -cp 1AKI_newbox.gro Input, Opt! Structure file: gro g96 pdb tpr etc. -cs spc216.gro Input, Opt!, Lib. Structure file: gro g96 pdb tpr etc. -ci insert.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -o solvated.gro Output Structure file: gro g96 pdb etc. -p topol.top In/Out, Opt! Topology file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -box vector 0 0 0 Box size -nmolint0 Number of extra molecules to insert -try int10 Try inserting -nmol times -try times -seedint1997Random generator seed -vdwdreal 0.105 Default van der Waals distance -shell real 0 Thickness of optional water layer around solute -maxsol int0 Maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored -[no]vel bool no Keep velocities from input solute and solvent Reading solute configuration LYSOZYME Containing 2194 atoms in 207 residues Initialising van der waals distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 4x4x4 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 13824 residues Calculating Overlap... box_margin = 0.315 Removed 0 atoms that were outside the box 1587-119 Error: Invalid number of threads defined. Why does the system returns the Error: Invalid number of threads defined? Best Regards Lukasz -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] genbox_mpi and Error: Invalid number of threads defined
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 and waiting for resources srun: job 5026 has been allocated resources :-) G R O M A C S (-: Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) /opt/gromacs/4.6.3/bin/genbox_mpi (-: Option Filename Type Description -cp 1AKI_newbox.gro Input, Opt! Structure file: gro g96 pdb tpr etc. -cs spc216.gro Input, Opt!, Lib. Structure file: gro g96 pdb tpr etc. -ci insert.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -o solvated.gro Output Structure file: gro g96 pdb etc. -p topol.top In/Out, Opt! Topology file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -box vector 0 0 0 Box size -nmolint0 Number of extra molecules to insert -try int10 Try inserting -nmol times -try times -seedint1997Random generator seed -vdwdreal 0.105 Default van der Waals distance -shell real 0 Thickness of optional water layer around solute -maxsol int0 Maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored -[no]vel bool no Keep velocities from input solute and solvent Reading solute configuration LYSOZYME Containing 2194 atoms in 207 residues Initialising van der waals distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 4x4x4 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 13824 residues Calculating Overlap... box_margin = 0.315 Removed 0 atoms that were outside the box 1587-119 Error: Invalid number of threads defined. Why does the system returns the Error: Invalid number of threads defined? None of the tools are MPI-aware. The error is probably a result of incorrect compilation. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] hints for core/shell optimization?
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 is an X-Y-X angle force type which does have an effect on forces and energy. Shell particles, on the other hand, are defined via the [polarization] section as quasi-bonds. That's all. Coulombic interactions fail at short distances; you probably need to apply Thole screening to avoid polarization catastrophe. Ions are particularly problematic in this regard. Try nstlist = 1. The shell positions are solved via SCF (EM), so you need to update the neighbor list very frequently. Thanks for the trick. Tried but to no avail (very same results). Although shells should have their weight in the model, I expect them not to frequently change partner -each is ultimately connected to its core atomic site. In addition, there are no more bonds in the system i, thus, don't see the point in regenerating pairs. Is there a process -I should get to know about- which autogenerates bonds? If your model doesn't use them, then there's nothing to be done here. I was asking about bonded structure and exclusions and such because of the Thole issue I noted above. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] hints for core/shell optimization?
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 effect on forces and energy. Shell particles, on the other hand, are defined via the [polarization] section as quasi-bonds. That's all. Try nstlist = 1. The shell positions are solved via SCF (EM), so you need to update the neighbor list very frequently. Thanks for the trick. Tried but to no avail (very same results). Although shells should have their weight in the model, I expect them not to frequently change partner -each is ultimately connected to its core atomic site. In addition, there are no more bonds in the system i, thus, don't see the point in regenerating pairs. Is there a process -I should get to know about- which autogenerates bonds? Thanks al lot for you help. Best regards, toma -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] hints for core/shell optimization?
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 screening to avoid polarization catastrophe. Ions are particularly problematic in this regard. I've seen this mentioned in the Manual, but hadn't ever hit GROMACS specific details on how to apply polarization in the input files. The only source I could locate is within the GROMACS package, under the name sw.itp. It does exclusively implement the so called water polarization model -at least I think so. Can you please direct me to a source from which I could learn how to polarize GROMACS? I was'not lucky on the Internet and, indeed, even at the GROMACS site or Manual (neighter application examples nor file format descriptions). I appreciate your help so much. With regards, toma -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs performance on virtual servers
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. However, for GROMACS the ideal scenario is exclusive host access (including hypervisor) and thread affinities which will both depend on the hypervisor configuration. Hence, if you can, you should try to get access to virtual hosts that fully utilize a compute node and do not share it with others. Definitely. On Fri, Jul 25, 2014 at 12:31 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Except for huge simulation systems, GROMACS performance past a single node is dominated by network latency, so unless you can extract a promise that any multi-node runs will have Infiniband-quality latency (because the nodes are physically in the same room, and on Infiniband) you can forget about doing multi-node MD on such a system. Two remarks: * With a slow network the only parallelization you can potentially make use of is multi-sim, unless your environment is so could-y that some nodes can have tens to hundreds of ms latency which can kill even you multi-sim performance (depending on how fast each simulation is and how often do they sync). I would not encourage multi-sim on such a setup, unless you actually want replica exchange. The multi-sim implementation unnecessarily syncs simulations every min(nstlist,nstcalcenergy,nstreplex) step, so that might be ~tens of times per second. Unnecessary multi-sim is good for pretending you are doing a big parallel calculation to get access to a large chunk of a machine, but this is not really the case here. Good point, I fully agree! What I meant was that one can use quite efficiently even cheap Ethernet networks for multi-sim type workloads where there is genuine need for communication between simulations (but not too often). For instance, replica exchange type runs work quite OK. -- Szilárd * I've seen several claims that *good* 10/40G Ethernet can get close to IB even in latency, even for MD, and even for GROMACS, e.g: http://goo.gl/JrNxKf, http://goo.gl/t0z15f Interesting, thanks. Mark Cheers, -- Szilárd Mark On Thu, Jul 24, 2014 at 10:54 PM, Elton Carvalho elto...@if.usp.br wrote: Dear Gromacs Users, My former university is focusing on cloud computing instead of physical servers, so research groups are now expected to buy virtual servers from the university coloud instead of buying their own clusters. The current setup employs Xeon E7- 2870 servers and there is an university-wide virtual cluster with 50 virtual servers each with 10 CPUs. Does anyone here have information on gromacs performance on this kind of infrastructure? Should I expect big issues? One thing that comes to mind is that the CPUs may not necessarily be in the same physical server, rack, or even datacenter (their plan is to decentralize the colocation), so network latency may be higher than the traditional setup, which may affect scaling. Does this argument make sense or am I missing something on cloud management 101? Cheers. -- Elton Carvalho Departamento de Física Universidade Federal do Paraná -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *
Re: [gmx-users] time accounting in log file with GPU
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 -resetstep options. Do they exclude the time spent on initialization and load-balancing from the total time reported in the log file, i.e., the time reported is the total time spent only in the loop/iterations over time-steps? Thanks, Sikandar On Thu, Jul 24, 2014 at 4:30 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Fri, Jul 25, 2014 at 12:48 AM, Sikandar Mashayak symasha...@gmail.com wrote: Thanks Mark. -noconfout option helps. For benchmarking purposes, additionally to -noconfout I suggest also using: * -resethway or -resetstep: to exclude initialization and load-balancing at the beginning of the run to get a more realistic performance measurement from a short run * -nsteps N or -maxh: the former is useful if you want to directly compare (e.g. two-sided diff) the timings from the end of the log between multiple runs Cheers, -- Szilárd -- Sikandar On Thu, Jul 24, 2014 at 3:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Fri, Jul 25, 2014 at 12:12 AM, Sikandar Mashayak symasha...@gmail.com wrote: Hi I am running a benchmark test with the GPU. The system consists of simple LJ atoms. And I am running only very basic simulation with NVE ensemble and not writing any trajectories or energy values. My grompp.mdp file is attached below. However, in the time accounting table in the md.log, I observe that write traj. and comm energies operations take 40% of time each. So, my question is that even if I have specified not to write trajectories and energies, why is 80% of time being spent on those operations? Because you're writing a checkpoint file (hint, use mdrun -noconfout), and that load is imbalanced so the other cores wait for it in the global communication stage in Comm. energies (fairly clear, since they have the same Wall time). Hint - make benchmarks run for about a minute, so you are not dominated by setup and load-balancing time. Your compute time was about 1/20 of a second... Mark Thanks, Sikandar R E A L C Y C L E A N D T I M E A C C O U N T I N G On 2 MPI ranks Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum % - Domain decomp. 21 11 0.006 0.030 2.1 DD comm. load 21 2 0.000 0.000 0.0 Neighbor search21 11 0.007 0.039 2.7 Launch GPU ops.21202 0.007 0.036 2.5 Comm. coord. 21 90 0.002 0.013 0.9 Force 21101 0.001 0.003 0.2 Wait + Comm. F 21101 0.004 0.020 1.4 Wait GPU nonlocal 21101 0.004 0.020 1.4 Wait GPU local 21101 0.000 0.002 0.2 NB X/F buffer ops. 21382 0.001 0.008 0.6 Write traj.21 1 0.108 0.586 40.2 Update 21101 0.005 0.025 1.7 Comm. energies 21 22 0.108 0.588 40.3 Rest 0.016 0.087 5.9 - Total 0.269 1.459 100.0 - grompp.mdp file: integrator = md-vv dt = 0.001 nsteps = 100 nstlog = 0 nstcalcenergy= 0 cutoff-scheme= verlet ns_type = grid nstlist = 10 pbc = xyz rlist= 0.7925 vdwtype = Cut-off rvdw = 0.7925 rcoulomb = 0.7925 gen_vel = yes gen_temp = 296.0 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For
Re: [gmx-users] time accounting in log file with GPU
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, Sikandar Mashayak symasha...@gmail.com wrote: Thanks Szilárd. I am bit confused about the -resethway or -resetstep options. Do they exclude the time spent on initialization and load-balancing from the total time reported in the log file, i.e., the time reported is the total time spent only in the loop/iterations over time-steps? Thanks, Sikandar On Thu, Jul 24, 2014 at 4:30 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Fri, Jul 25, 2014 at 12:48 AM, Sikandar Mashayak symasha...@gmail.com wrote: Thanks Mark. -noconfout option helps. For benchmarking purposes, additionally to -noconfout I suggest also using: * -resethway or -resetstep: to exclude initialization and load-balancing at the beginning of the run to get a more realistic performance measurement from a short run * -nsteps N or -maxh: the former is useful if you want to directly compare (e.g. two-sided diff) the timings from the end of the log between multiple runs Cheers, -- Szilárd -- Sikandar On Thu, Jul 24, 2014 at 3:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Fri, Jul 25, 2014 at 12:12 AM, Sikandar Mashayak symasha...@gmail.com wrote: Hi I am running a benchmark test with the GPU. The system consists of simple LJ atoms. And I am running only very basic simulation with NVE ensemble and not writing any trajectories or energy values. My grompp.mdp file is attached below. However, in the time accounting table in the md.log, I observe that write traj. and comm energies operations take 40% of time each. So, my question is that even if I have specified not to write trajectories and energies, why is 80% of time being spent on those operations? Because you're writing a checkpoint file (hint, use mdrun -noconfout), and that load is imbalanced so the other cores wait for it in the global communication stage in Comm. energies (fairly clear, since they have the same Wall time). Hint - make benchmarks run for about a minute, so you are not dominated by setup and load-balancing time. Your compute time was about 1/20 of a second... Mark Thanks, Sikandar R E A L C Y C L E A N D T I M E A C C O U N T I N G On 2 MPI ranks Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum % - Domain decomp. 21 11 0.006 0.030 2.1 DD comm. load 21 2 0.000 0.000 0.0 Neighbor search21 11 0.007 0.039 2.7 Launch GPU ops.21202 0.007 0.036 2.5 Comm. coord. 21 90 0.002 0.013 0.9 Force 21101 0.001 0.003 0.2 Wait + Comm. F 21101 0.004 0.020 1.4 Wait GPU nonlocal 21101 0.004 0.020 1.4 Wait GPU local 21101 0.000 0.002 0.2 NB X/F buffer ops. 21382 0.001 0.008 0.6 Write traj.21 1 0.108 0.586 40.2 Update 21101 0.005 0.025 1.7 Comm. energies 21 22 0.108 0.588 40.3 Rest 0.016 0.087 5.9 - Total 0.269 1.459 100.0 - grompp.mdp file: integrator = md-vv dt = 0.001 nsteps = 100 nstlog = 0 nstcalcenergy= 0 cutoff-scheme= verlet ns_type = grid nstlist = 10 pbc = xyz rlist= 0.7925 vdwtype = Cut-off rvdw = 0.7925 rcoulomb = 0.7925 gen_vel = yes gen_temp = 296.0 -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] hints for core/shell optimization?
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 (with not yet reasonable results). Thole screening to avoid polarization catastrophe. Ions are particularly problematic in this regard. I've seen this mentioned in the Manual, but hadn't ever hit GROMACS specific details on how to apply polarization in the input files. The only source I could locate is within the GROMACS package, under the name sw.itp. It does exclusively implement the so called water polarization model -at least I think so. The water polarization function is a water-specific anisotropy function. Don't try to use it for anything else; the interpretation of the atom numbers for local axis construction are very specific. Can you please direct me to a source from which I could learn how to polarize GROMACS? I was'not lucky on the Internet and, indeed, even at the GROMACS site or Manual (neighter application examples nor file format descriptions). The Thole screening function is (in the released version) not used by anything, so it's not documented. In its present incarnation, you need a [thole_polarization] directive that lists atom-shell/Drude pairs as follows: atom_i shell_i atom_j shell_j 2 a alpha_i alpha_j The 2 is a required function type. My implementation of the CHARMM Drude FF is nearly done, and there are changes to the way the Thole directive is laid out in the future, but at the moment (up through version 5.0), this is the way it works. The code is in src/gromacs/gmxlib/bondfree.c. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Can't run v. 4.6.6 on worker nodes if they are compiled with SIMD
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 (v6.0). I can not make this work if I compile GROMACS with SIMD, no matter what kernel I choose - I have tried everything from SSE2 to AVX_256. The log-in node, where I compile, has AMD Interlagos CPUs (worker nodes use Xeon E5-2630 and are equipped with Tesla K20), but I do not think this is the problem - I have compiled GROMACS, using the log-in node, without CUDA but with AVX_256 SIMD and everything works. As soon as CUDA is added to the mix, I get Illegal Instruction every time I try to run on the worker nodes. Compiling on worker nodes gives the same result. However, as soon as I set SIMD=None everything works and I am able to run simulation using GPUs, this is regardless of if I use log-in node or worker node to compile. The cmake string used to configure is: ccmake .. -DCMAKE_INSTALL_PREFIX=/work/gromacs4gpu -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_4gpu -DGMX_LIBS_SUFFIX=_4gpu -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -GMX_MPI=OFF -DGMX_CPU_ACCELERATION=AVX_256 CUDA v6.0 and FFTW v3.3.4 (single precision) libs are set globally and correctly identified by GROMACS. To remove OpenMPI as a problem I am compiling without it (compiling with OpenMPI produced the same behavior as without), once I have found the error I will compile with OpenMPI v1.6.5. I get these warnings during the configuration, nothing important: A BLAS library was not found by CMake in the paths available to it. Falling back on the GROMACS internal version of the BLAS library instead. This is fine for normal usage. A LAPACK library was not found by CMake in the paths available to it. Falling back on the GROMACS internal version of the LAPACK library instead. This is fine for normal usage. I am currently trying to compile and test GROMACS 5.0 to see if it also exhibits the same behavior. I hope that someone can point me in the direction of a possible solution, if not then I will file a bug report. Regards, Mohtadin Forgot to attached the md.log. Please find attached md.log for both v4.6.6 and v5.0 The list does not accept attachments. Please post the files somewhere for download. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Can't run v. 4.6.6 on worker nodes if they are compiled with SIMD
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 compile GROMACS with CUDA (v6.0). I can not make this work if I compile GROMACS with SIMD, no matter what kernel I choose - I have tried everything from SSE2 to AVX_256. The log-in node, where I compile, has AMD Interlagos CPUs (worker nodes use Xeon E5-2630 and are equipped with Tesla K20), but I do not think this is the problem - I have compiled GROMACS, using the log-in node, without CUDA but with AVX_256 SIMD and everything works. As soon as CUDA is added to the mix, I get Illegal Instruction every time I try to run on the worker nodes. Compiling on worker nodes gives the same result. However, as soon as I set SIMD=None everything works and I am able to run simulation using GPUs, this is regardless of if I use log-in node or worker node to compile. The cmake string used to configure is: ccmake .. -DCMAKE_INSTALL_PREFIX=/work/gromacs4gpu -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_4gpu -DGMX_LIBS_SUFFIX=_4gpu -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -GMX_MPI=OFF -DGMX_CPU_ACCELERATION=AVX_256 CUDA v6.0 and FFTW v3.3.4 (single precision) libs are set globally and correctly identified by GROMACS. To remove OpenMPI as a problem I am compiling without it (compiling with OpenMPI produced the same behavior as without), once I have found the error I will compile with OpenMPI v1.6.5. I get these warnings during the configuration, nothing important: A BLAS library was not found by CMake in the paths available to it. Falling back on the GROMACS internal version of the BLAS library instead. This is fine for normal usage. A LAPACK library was not found by CMake in the paths available to it. Falling back on the GROMACS internal version of the LAPACK library instead. This is fine for normal usage. I am currently trying to compile and test GROMACS 5.0 to see if it also exhibits the same behavior. I hope that someone can point me in the direction of a possible solution, if not then I will file a bug report. Regards, Mohtadin Forgot to attached the md.log. Please find attached md.log for both v4.6.6 and v5.0 Unfortunately, v5.0 seems to exhibit the same behavior as v4.6.6. The logs: 4.6.6: http://pastebin.com/vxagEEZC 5.0: http://pastebin.com/eMemFq1J -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] electrostatics forces and van der waals forces calculation
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 the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
