[gmx-users] amber ff gromacs
Dear People, I am trying to simulate glycine molecule using amber ff. I have changed the residues in pdb file with N and C respectively. ATOM 1 NNGLY1 -1.476 0.232 0.252 1.00 0.00 ATOM 2 CA CGLY1 -0.012 0.296 0.348 1.00 0.00 ATOM 3 CCGLY1 0.596 -0.652 -0.648 1.00 0.00 ATOM 4 O GLY 1 -0.124 -1.320 -1.368 1.00 0.00 ATOM 5 OXT GLY 1 1.916 -0.760 -0.740 1.00 0.00 ATOM 6 H3 GLY 1 -1.736 -0.252 -0.592 1.00 0.00 ATOM 7 HA2 GLY 1 0.292 0.020 1.364 1.00 0.00 ATOM 8 HA1 GLY 1 0.320 1.320 0.132 1.00 0.00 ATOM 9 HGLY 1 -1.636 -0.236 1.132 1.00 0.00 ATOM 10 H GLY 1 -1.916 1.136 0.272 1.00 0.00 TER 11 GLY 1 END But when I am using pdb2gmx, I am getting this error Residue 1 named NGLY of a molecule in the input file was mapped to an entry in the topology database, but the atom CA used in that entry is not found in the input file. But atom CA is in the input pdb file and with same name in amber .rtp file too. If I remove N and C prefixes in pdb file, pdb works for all other fields. I will be thankful for your help and time. Kind Regards, Amninder Virk -- View this message in context: http://gromacs.5086.x6.nabble.com/amber-ff-gromacs-tp5015342.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] refcoord-scaling
On Mar 24, 2014 1:10 AM, Chetan Mahajan chetanv...@gmail.com wrote: Dear all: I am trying to get a simulation of water solvated titanium oxide running. When 'all' option is used for refcoord-scaling, simulation runs ok. However, when 'com' option is used for refcoord-scaling, simulation crashes with any of the following errors. Could anyone explain to me why is this happening See the description of com. You didn't tell us what you were restraining, so it's hard to help. But I can see multiple com of tio2 and PBC not working well together, particularly if you box size is far from best. or when each of the options such as 'all', 'com' and 'no' is used? When you really care about your starting position and need to equilibrate in NPT. Mark Thanks a lot! regards Chetan Errors: X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group This is another way that mdrun tells you your system is blowing uphttp://www.gromacs.org/Documentation/Terminology/Blowing_Up. In GROMACS version 4.0, domain decomposition was introduced to divide the system into regions containing nearby atoms (for more details, see the manual http://www.gromacs.org/Documentation/Manual or the GROMACS 4 paperhttp://dx.doi.org/10.1021/ct700301q). If you have particles that are flying across the system, you will get this fatal error. The message indicates that some piece of your system is tearing apart (hence out of the cell of their charge group). Refer to the Blowing Up http://www.gromacs.org/Documentation/Terminology/Blowing_Up page for advice on how to fix this issue. A charge group moved too far between two domain decomposition steps. -- 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] Add atom to .itp file
I don't understand your description. Mark On Mar 24, 2014 4:09 AM, deep satyadeep.r...@gmail.com wrote: I want to create a polarizable particle system consisting of a sphere carying charge q and some size r1 on which a oppositively charge -q is present with some other size r2 . Overall I want to create a colloidal particle . Can anyone please help me in making these sphere (atom ) in itp file ? I want to write some command and I don't know what exactly I have to write . Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/Add-atom-to-itp-file-tp5015341.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Error: illegal instruction (core dumped)
@Mark Abraham: I have received your email but because I don't see it on the thread so I think you deleted your answer. Sorry about that. I'm still new with the mail list. Anyway, I have already deleted the build folder and make a fresh install but it doesn't solve. @Justin Lemkul: my machine is Intel Pentium P6200 (2.13 GHz, 3 MB L3 cache). Any cmake command leads to the same error. So if you want a specific command, let's use the simplist one:* cmake ..* I know that I optimized it wrong, but how can I fix that? On Mon, Mar 24, 2014 at 6:11 AM, Justin Lemkul [via GROMACS] ml-node+s5086n5015337...@n6.nabble.com wrote: On 3/23/14, 11:57 AM, ooker wrote: sorry for spamming, but I need to up this thread. I'll delete this after someone answer. Sorry. You'll need to provide exact details of your hardware and your exact cmake command, otherwise there's nothing productive to suggest. The build machinery is good at picking the correct optimization type, so the only real issue is if you're selecting an optimization that is not supported. -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 [hidden email] http://user/SendEmail.jtp?type=nodenode=5015337i=0 | (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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5015337i=1. -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/Error-illegal-instruction-core-dumped-tp5015293p5015337.html To unsubscribe from Error: illegal instruction (core dumped), click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5015293code=Z2FudW9uZ3BoYXBAZ21haWwuY29tfDUwMTUyOTN8MjA5NTYxNDQyOQ== . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://gromacs.5086.x6.nabble.com/Error-illegal-instruction-core-dumped-tp5015293p5015343.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] free energy of removal of a molecule from the bulk
Thank you Justin. This is what I have tried, but obviously gone wrong with [settles]. I'll try again. V -- View this message in context: http://gromacs.5086.x6.nabble.com/free-energy-of-removal-of-a-molecule-from-the-bulk-tp5015333p5015344.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Add atom to .itp file
I want to make a new itp file and add two atoms in it. Something like this ;[atoms] 1a1 q r1 2 a2 -q r2 On Mon, Mar 24, 2014 at 2:47 PM, Mark Abraham mark.j.abra...@gmail.comwrote: I don't understand your description. Mark On Mar 24, 2014 4:09 AM, deep satyadeep.r...@gmail.com wrote: I want to create a polarizable particle system consisting of a sphere carying charge q and some size r1 on which a oppositively charge -q is present with some other size r2 . Overall I want to create a colloidal particle . Can anyone please help me in making these sphere (atom ) in itp file ? I want to write some command and I don't know what exactly I have to write . Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/Add-atom-to-itp-file-tp5015341.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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. -- *Satyadeep roat* Undergraduate Student, Department of Chemical Engineering, IIT Delhi Email- satyadeep.r...@gmail.com Mobile- +91 8527211721 -- 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] Error: illegal instruction (core dumped)
On 3/24/14, 5:32 AM, ooker wrote: @Mark Abraham: I have received your email but because I don't see it on the thread so I think you deleted your answer. Sorry about that. I'm still new with the mail list. Anyway, I have already deleted the build folder and make a fresh install but it doesn't solve. @Justin Lemkul: my machine is Intel Pentium P6200 (2.13 GHz, 3 MB L3 cache). Any cmake command leads to the same error. So if you want a specific command, let's use the simplist one:* cmake ..* I know that I optimized it wrong, but how can I fix that? It's still not clear. Simply running cmake and nothing else relies on a lot of assumptions - does it work? Does it give an error? What level of optimization does cmake detect? As for hardware, what is the output of `cat /proc/cpuinfo` and what C compiler are you using? -Justin On Mon, Mar 24, 2014 at 6:11 AM, Justin Lemkul [via GROMACS] ml-node+s5086n5015337...@n6.nabble.com wrote: On 3/23/14, 11:57 AM, ooker wrote: sorry for spamming, but I need to up this thread. I'll delete this after someone answer. Sorry. You'll need to provide exact details of your hardware and your exact cmake command, otherwise there's nothing productive to suggest. The build machinery is good at picking the correct optimization type, so the only real issue is if you're selecting an optimization that is not supported. -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 [hidden email] http://user/SendEmail.jtp?type=nodenode=5015337i=0 | (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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5015337i=1. -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/Error-illegal-instruction-core-dumped-tp5015293p5015337.html To unsubscribe from Error: illegal instruction (core dumped), click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5015293code=Z2FudW9uZ3BoYXBAZ21haWwuY29tfDUwMTUyOTN8MjA5NTYxNDQyOQ== . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://gromacs.5086.x6.nabble.com/Error-illegal-instruction-core-dumped-tp5015293p5015343.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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] MPI error in gromacs 4.6
Hello Ankita You have to just include the following line in your mdp file cutoff-scheme=Verlet And run your grompp with the modfied mdp file to generate tpr file and then mdrun. Hope this doesn't give you the same error On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 318 318; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen; Berendsen thermostat pcoupltype= isotropic; uniform scaling of box vectors tau_p= 1.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; Velocity generation is on gen_temp= 318; reference temperature, for protein in K Kind regards-- Ankita Naithani -- 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
Re: [gmx-users] MPI error in gromacs 4.6
Hi Pavan, Thank you for your response. I am trying to generate the tpr file with the following parameter; ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter file. On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar kumar.pavan...@gmail.comwrote: Hello Ankita You have to just include the following line in your mdp file cutoff-scheme=Verlet And run your grompp with the modfied mdp file to generate tpr file and then mdrun. Hope this doesn't give you the same error On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 318 318; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen; Berendsen thermostat
Re: [gmx-users] MPI error in gromacs 4.6
It might be some typographical errors. Check the mdp file thoroughly. I think semicolon is required for the last line in your mdp file On Mon, Mar 24, 2014 at 5:18 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi Pavan, Thank you for your response. I am trying to generate the tpr file with the following parameter; ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter file. On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar kumar.pavan...@gmail.com wrote: Hello Ankita You have to just include the following line in your mdp file cutoff-scheme=Verlet And run your grompp with the modfied mdp file to generate tpr file and then mdrun. Hope this doesn't give you the same error On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale;
Re: [gmx-users] MPI error in gromacs 4.6
On Mon, Mar 24, 2014 at 12:17 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. You should need to do that kind of thing only for equilibration, e.g. see http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. If you want to run with the group scheme, use cutoff-scheme = group, control your job script to use an MPI rank per core, and do not attempt to use OpenMP. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Many things are different, but if you're confident no relevant bugs were fixed, you can use 4.6.x to do the same things as 4.5.5 could do. But since such runs would not have http://www.gromacs.org/Documentation/Terminology/Reproducibility, then they will not have continuity either. Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 318 318; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen; Berendsen thermostat pcoupltype= isotropic; uniform scaling of box vectors tau_p= 1.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity
Re: [gmx-users] MPI error in gromacs 4.6
On Mon, Mar 24, 2014 at 12:48 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi Pavan, Thank you for your response. I am trying to generate the tpr file with the following parameter; ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter file. If you want to prepare a run for GROMACS 4.6, use a 4.6 version of grompp! Mark On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar kumar.pavan...@gmail.com wrote: Hello Ankita You have to just include the following line in your mdp file cutoff-scheme=Verlet And run your grompp with the modfied mdp file to generate tpr file and then mdrun. Hope this doesn't give you the same error On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps=
Re: [gmx-users] MPI error in gromacs 4.6
On 3/24/14, 7:48 AM, Ankita Naithani wrote: Hi Pavan, Thank you for your response. I am trying to generate the tpr file with the following parameter; ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter file. That option was introduced in version 4.6. It won't work with an earlier version. -Justin On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar kumar.pavan...@gmail.comwrote: Hello Ankita You have to just include the following line in your mdp file cutoff-scheme=Verlet And run your grompp with the modfied mdp file to generate tpr file and then mdrun. Hope this doesn't give you the same error On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 318 318; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen; Berendsen thermostat pcoupltype=
Re: [gmx-users] MPI error in gromacs 4.6, more Errors
On 3/24/14, 7:57 AM, Ankita Naithani wrote: Hi, so I modified my mdp file which now looks like the following: title= production MD ; Run parameters integrator= md; leap-frog algorithm ;nsteps= 2000; 0.005 * 2000 = 10 ps or 100 ns ;nsteps= 20; 0.005 * 20 = 1 ns ;dt= 0.005; 5 fs nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 318 318; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen; Berendsen thermostat pcoupltype= isotropic; uniform scaling of box vectors tau_p= 1.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; Velocity generation is on gen_temp= 318; reference temperature, for protein in K -- But, when I try to generate the tpr file on the cluster itself using gromacs 4.6.3, I get the following error: NOTE 1 [file md3.mdp]: With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file md3.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy Generated 3403 of the 3403 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3403 of the 3403 1-4 parameter combinations Segmentation fault Can anyone please suggest further? Do as the notes suggest. They're not fatal errors, they're just cautionary. You should probably educate yourself a bit further on what all of these algorithms are by taking a look at http://www.gromacs.org/Documentation/Cut-off_schemes. The Verlet scheme is not mandatory, but it is required by the type of parallelization you requested. Reviewers may question the changes in version and cutoff methods when critiquing your work, so be aware of that. Also, the instability you are seeing is probably a result of the large time step, unless you are using virtual sites. -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] Protein-Ligand MS simulation
Hello. I have a protein pdb and the best pose of a ligand obtained through docking using auto dock. However, when I combine the ligand and protein using the discovery studio, some residues like Lysine in the protein pdb gets protonated as well as the N-terminal residue. Is this unusual and can it affect the MD end results? -- 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] Protein-Ligand MS simulation
On 3/24/14, 8:52 AM, MUSYOKA THOMMAS wrote: Hello. I have a protein pdb and the best pose of a ligand obtained through docking using auto dock. However, when I combine the ligand and protein using the discovery studio, some residues like Lysine in the protein pdb gets protonated as well as the N-terminal residue. Is this unusual and can it affect the MD end results? I can't speak to what's usual in Discovery Studio (and there's probably a better forum for that, anyway), but it seems like it's just assuming standard (pH 7) protonation states. Both lysine and the N-terminus are predominantly protonated at neutral pH. Protonation state can have a major impact on the outcome of a simulation, especially in binding sites, and should be chosen wisely. -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] MPI error in gromacs 4.6, more Errors
The segmentation fault is highly unusual, and suggests that the installation of gromacs used a shared library that has now migrated/changed/whatever. I suggest you discuss that with your system admins and ask them to re-install, or re-run the GROMACS regression tests, to check things are OK. Mark On Mon, Mar 24, 2014 at 2:13 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi Justin, Thank you very much for your reply. I shall try to work my way around and see. Kind regards, Ankita On Mon, Mar 24, 2014 at 12:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/24/14, 7:57 AM, Ankita Naithani wrote: Hi, so I modified my mdp file which now looks like the following: title= production MD ; Run parameters integrator= md; leap-frog algorithm ;nsteps= 2000; 0.005 * 2000 = 10 ps or 100 ns ;nsteps= 20; 0.005 * 20 = 1 ns ;dt= 0.005; 5 fs nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 318 318; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen; Berendsen thermostat pcoupltype= isotropic; uniform scaling of box vectors tau_p= 1.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; Velocity generation is on gen_temp= 318; reference temperature, for protein in K -- But, when I try to generate the tpr file on the cluster itself using gromacs 4.6.3, I get the following error: NOTE 1 [file md3.mdp]: With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 2 [file md3.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy Generated 3403 of the 3403 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 3403 of the 3403 1-4 parameter combinations Segmentation fault Can anyone please suggest further? Do as the notes suggest. They're not fatal errors, they're just cautionary. You should probably educate yourself a bit further on what all of these algorithms are by taking a look at http://www.gromacs.org/ Documentation/Cut-off_schemes. The Verlet scheme is not mandatory, but it is required by the type of parallelization you requested. Reviewers may question the changes in version and cutoff methods when critiquing your work, so be aware of that. Also, the instability you are seeing is probably a result of the large time step, unless you are using virtual sites. -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
Re: [gmx-users] refcoord-scaling
Hi Mark, I am restraining positions of each of the atoms of TiO2 crystal. Could you comment again why should simulation crash when 'com' option is used against 'all' option? Also, description in the manual does not answer my question: when is 'all' option generally used? When is 'com' option generally used? When is 'no' option generally used? Thanks! regards Chetan On Mon, Mar 24, 2014 at 4:16 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Mar 24, 2014 1:10 AM, Chetan Mahajan chetanv...@gmail.com wrote: Dear all: I am trying to get a simulation of water solvated titanium oxide running. When 'all' option is used for refcoord-scaling, simulation runs ok. However, when 'com' option is used for refcoord-scaling, simulation crashes with any of the following errors. Could anyone explain to me why is this happening See the description of com. You didn't tell us what you were restraining, so it's hard to help. But I can see multiple com of tio2 and PBC not working well together, particularly if you box size is far from best. or when each of the options such as 'all', 'com' and 'no' is used? When you really care about your starting position and need to equilibrate in NPT. Mark Thanks a lot! regards Chetan Errors: X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group This is another way that mdrun tells you your system is blowing uphttp://www.gromacs.org/Documentation/Terminology/Blowing_Up. In GROMACS version 4.0, domain decomposition was introduced to divide the system into regions containing nearby atoms (for more details, see the manual http://www.gromacs.org/Documentation/Manual or the GROMACS 4 paperhttp://dx.doi.org/10.1021/ct700301q). If you have particles that are flying across the system, you will get this fatal error. The message indicates that some piece of your system is tearing apart (hence out of the cell of their charge group). Refer to the Blowing Up http://www.gromacs.org/Documentation/Terminology/Blowing_Up page for advice on how to fix this issue. A charge group moved too far between two domain decomposition steps. -- 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] Umbrella pulling Drug + Ion channel
Dear gromacs users, i ´ve beem trying to get the geometries of a drug molecule permeating an ion channel, the drug molecule is in a greater Z position than the Protein, but i always get the error :Segmentation fault (core dumped) this is my .mdp title = Umbrella pulling simulation DOX ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 cutoff-scheme = Verlet ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 20 ns_type = grid rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein POPC Water_and_ions_DOX tau_t = 1.01.0 1.0 ref_t = 310310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = cylinder ; pull_vec1 = 0.0 0.0 1.0 ; pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Protein pull_group1 = DOX pull-r1 = 1.0 pull-r0 = 1.0 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 800 ; kJ mol^-1 nm^-2 pull_pbcatom0 = 8485 According with other post, i have to select a pull_pbcatom0 closes to the middle of my reference ( an atom close to the middle of the ion channel's pore) and a pull_vec1 positive even if the drug is above the channel, i was wondering if you could help me with this, or giving me an advice of this error, thanks in advance Andrés Ortega -- View this message in context: http://gromacs.5086.x6.nabble.com/Umbrella-pulling-Drug-Ion-channel-tp5015363.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] refcoord-scaling
Hi Justin, My system is TiO2 crystal (2160 atoms position restrained) solvated by 3656 water molecules, 1 formate anion and 1 sodium ion. Is it true that when 'all' option is used, positions of the atoms (meant to be restrained) always change? Thanks Chetan On Mon, Mar 24, 2014 at 7:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/24/14, 8:29 PM, Chetan Mahajan wrote: Thanks, Mark. So is 'all' option okay when positions of each of the atoms of TiO2 crystal (2160 atoms total) are restrained in space? Apparently, it does not seem correct, since positions of the atoms of TiO2 crystal change when 'all' option is applied. However, it does not give error as 'com' option does. Is your system just a TiO2 crystal? Is there any solvent? If it's just a crystal, I see no point in restraining anything. It is very unusual that the all option of refcoord-scaling is more stable than com - normally the opposite is true. But that also explains why the coordinates are changing - the reference position of each individual atom is scaled according to the pressure coupling matrix, so the atoms are restrained to a dynamic reference, so it seems that it's not really accomplishing anything. -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] refcoord-scaling
On 3/24/14, 9:05 PM, Chetan Mahajan wrote: Hi Justin, My system is TiO2 crystal (2160 atoms position restrained) solvated by 3656 water molecules, 1 formate anion and 1 sodium ion. Is it true that when 'all' option is used, positions of the atoms (meant to be restrained) always change? Consider what position restraints are doing. They never guarantee that atoms won't move; they just apply a biasing potential to disfavor movement. So yes, your atoms will probably move. The smaller the system, the larger the effect will likely be. Consider also what reference coordinates are doing. They define how strong the potential is (distance between current coordinates and reference). If you're scaling all atoms individually according to the pressure coupling, the reference moves and therefore the atoms can also move. For larger systems like proteins, refcoord_scaling = com is normal and stable, and refcoord_scaling = all is disfavored. Honestly, I don't know what to expect for a very small system like yours, but it is likely to be affected to a greater extent. If the all option gives you a stable simulation that allow for proper equilibration, then I doubt there is any real problem. -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] berger lipid parameters in amber99sb-ildn ff
Dear Chris Sorry, That didn't solve my problem. I tried that option ,before posting here, with different authors from two publications, but seems no reply from anybody. I wish, I could find somebody in this mailing list who is willing to put forward his/her advice or share their experience with me to solve this issue. Many thanks in advance. Message: 1 Date: Sun, 23 Mar 2014 11:32:44 + From: Christopher Neale chris.ne...@alum.utoronto.ca To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] berger lipid parameters in amber99sb-ildn ff Message-ID: 91dc2bfb46004e1b9fa1a8922bb55...@blupr03mb184.namprd03.prod.outlook.com Content-Type: text/plain; charset=us-ascii See this paper for Amber protein and berger lipids: http://pubs.acs.org/doi/abs/10.1021/ct200491c If you contact the authors, I am sure that they can send you the files. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Monoj Mon Kalita mon.123c...@gmail.com Sent: 23 March 2014 00:29 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] berger lipid parameters in amber99sb-ildn ff Dear Users I am trying to run a drug-protein simulation in GROMACS. I have calculated the ligand paramteres using the generalized amber force field (GAFF) . ESP partial charges were calculated using HF/6-31G* basis set. RESP fitting was performed using the Antechamber . Now I am having trouble in introducing the berger lipid parameters into the topology file created by amber99sb-ildn ff . All I got are gromos adopted forcefield files and berger lipid parameters as I want to run my simulation in united-atom POPC membrane with berger lipid parameter and amber99sb-ildn ff for protein. Is there any link to download the amber adopted toplogy file for united atom POPC with berger lipid forcefield parameters which may solve my problem. I am following the method mentioned in this publication doi: 10.3109/09687688.2013.773095. to set up my protocol. -- With Regards Monoj Mon Kalita Taipei, Taiwan -- With Regards Monoj Mon Kalita Taipei, Taiwan -- 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] refcoord-scaling
Thanks, Justin. I am trying to understand what is meant by 'com' option. Following two sentences in manual seem conflicting with each other: *Scale* the center of mass of the reference coordinates with the scaling matrix of the pressure coupling. The *vectors of each reference coordinate*to the center of mass are *not scaled*. Doesn't scaling center of mass of reference coordinates change something else ? reference coordinates? Thanks Chetan On Mon, Mar 24, 2014 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/24/14, 9:05 PM, Chetan Mahajan wrote: Hi Justin, My system is TiO2 crystal (2160 atoms position restrained) solvated by 3656 water molecules, 1 formate anion and 1 sodium ion. Is it true that when 'all' option is used, positions of the atoms (meant to be restrained) always change? Consider what position restraints are doing. They never guarantee that atoms won't move; they just apply a biasing potential to disfavor movement. So yes, your atoms will probably move. The smaller the system, the larger the effect will likely be. Consider also what reference coordinates are doing. They define how strong the potential is (distance between current coordinates and reference). If you're scaling all atoms individually according to the pressure coupling, the reference moves and therefore the atoms can also move. For larger systems like proteins, refcoord_scaling = com is normal and stable, and refcoord_scaling = all is disfavored. Honestly, I don't know what to expect for a very small system like yours, but it is likely to be affected to a greater extent. If the all option gives you a stable simulation that allow for proper equilibration, then I doubt there is any real problem. -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] refcoord-scaling
Say you have a box with an x-side length of 3 nm and two atoms with x-dimension position restraints to: (a) x=1 nm, and (b) x=2 nm Then let the box shrink to 99% of its previous size due to pressure coupling. The following is my understanding of the locations to which the atoms will be restrained: refcoord_scaling = none: (a) x=1 nm, and (b) x=2 nm -- note how the restraint positions are not scaled (even though the positions of the atoms are scaled due to pressure coupling) all: (a) x=0.99 nm, and (b) x=1.98 nm -- note how the atoms are now restrained to be closer together com: (a) x=0.985 nm, and (b) x=1.985 nm -- note how the distance between the atoms is maintained So you see how none leads to problems because the restraint reference positions are not scaled at all with the atomic positions and how all leads to problems because, if you restrained all Ca atoms, then you would get compression/expansion of the size of your protein as the system fluctuated in constant pressure simulations. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Chetan Mahajan chetanv...@gmail.com Sent: 24 March 2014 23:25 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] refcoord-scaling Thanks, Justin. I am trying to understand what is meant by 'com' option. Following two sentences in manual seem conflicting with each other: *Scale* the center of mass of the reference coordinates with the scaling matrix of the pressure coupling. The *vectors of each reference coordinate*to the center of mass are *not scaled*. Doesn't scaling center of mass of reference coordinates change something else ? reference coordinates? Thanks Chetan On Mon, Mar 24, 2014 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/24/14, 9:05 PM, Chetan Mahajan wrote: Hi Justin, My system is TiO2 crystal (2160 atoms position restrained) solvated by 3656 water molecules, 1 formate anion and 1 sodium ion. Is it true that when 'all' option is used, positions of the atoms (meant to be restrained) always change? Consider what position restraints are doing. They never guarantee that atoms won't move; they just apply a biasing potential to disfavor movement. So yes, your atoms will probably move. The smaller the system, the larger the effect will likely be. Consider also what reference coordinates are doing. They define how strong the potential is (distance between current coordinates and reference). If you're scaling all atoms individually according to the pressure coupling, the reference moves and therefore the atoms can also move. For larger systems like proteins, refcoord_scaling = com is normal and stable, and refcoord_scaling = all is disfavored. Honestly, I don't know what to expect for a very small system like yours, but it is likely to be affected to a greater extent. If the all option gives you a stable simulation that allow for proper equilibration, then I doubt there is any real problem. -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. -- 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.
