[gmx-users] Error when using mdrun_mpi
Hello all,I am using gromacs 2019, i installed openmpi and did the buil mdrun only option, however when i type the command mpirun -np 6 -v mdrun_mpi -multidir replica-[012345] -s 1a1z-md.tpr -x 1a1z-md.xtc -o 1a1z-md.trr -c 1a1z-md.pdb -replex 500i get the following errormpirun was unable to find the specified executable file, and therefore did not launch the job. This error was first reported for process rank 0; it may have occurred for other processes as well. NOTE: A common cause for this error is misspelling a mpirun command line parameter option (remember that mpirun interprets the first unrecognized command line token as the executable). Node: tesla Executable: mdrun_mpi -- 6 total processes failed to start can someone tell me how to solve this issue? why is the openmpi wrapper doesnt recognize the mdrun_mpi command from gromacs?Hanin -- 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] mdrun log file question
hello all,I am running an md simulation using gromacs 2019 with RDC restraints added in all steps, now in my log file i get something like this Orientation experiment 1: order parameter: -0.00156791 eig: 1.000 -0.085 0.037 0.996 eig: -0.636 -0.144 0.988 -0.049 eig: -0.364 0.986 0.148 0.079 Orientation experiment 2: order parameter: 0.00196219 eig: 1.000 0.497 0.569 0.655 eig: -0.596 0.785 0.027 -0.619 eig: -0.404 0.370 -0.822 0.434 so my question is what does the order parameter her represents, is it a scalling factor for the eigen values or something elsecan someone help me with thisThank youHanin OMar -- 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] Error in mdrun
Hi allI am trying to run md simulation of a 83 residue protein with AMBER99SB-ILDN protein forcefield and TIP3P water model, i am adding orientation restraint to my protein alone however when i run NVT equlibration i get this errorFatal error: Found 5384 copies of a molecule with orientation restrains while the current code only supports a single copy. If you want to ensemble average, run multiple copies of the system using the multi-sim feature of mdrun. To my understanding this means that gromacs is applying the RDC restraints on all water molecule which is weird cause in my topology file i added the restraint file before including the water topology like this:; Include RDC restraint file #include "RDC-restraint.itp" ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" also in my mdp file i have this section:;Options for orientation restraint orire = yes orire-fc = 1 ; Orientation restraints force constant orire-tau = 0 ; Turn off time averaging orire-fitgrp = backbone is their something i need to add so that gromacs apply the rdc restraint only on the protein.i really appreciate the helpThank you Hanin OMar -- 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] Updated REMD question
Hello everyone;I have posted a question earlier about REMD simulation but i got no answer so i am going to re-post it with ore detail hoping someone might give me a hint. My research focuses on detection and modeling of internal dynamics within proteins. My first attempts with gromacs focused on running normal md simulation with the addition of residual dipolar coupling data for the dynamics from NMR spectroscopy as an orientation restraint itp file added to all steps of the simulation ( energy minimization, nvt equiliberation, npt equiliberartion and md production) with the hopes that gromacs will be able to generate the right trajectory for the dynamics; as a result gromacs was able to detect the position of dynamics but failed in simulation the right trajectory, not to mention that some secondary structure information were lost. So the same procedure was repeated with the addition of dihedral restraint however the improvement was minor. So i read in some literature that some groups where able to identify and model 4 step dynamics by running REMD with distance restraint data, so i thought ill try that but with RDC data instead.My REMD simulation has 4 exact replicas each equiliberated in different temperature as in this tutorialAn introduction to replica exchange simulations: Mark Abraham, Session 1B - Gromacs, how ever i did npt equiliberation following the nvt part ( with all having the same pressure value).as a result i have 4 (log, edr,xtc) files for each replica, but when i try to visualized the trajectory for each replica not only do they differ from each other, i notice that in all of them the structure of the protein breaks, some bonds are so stretched that they leave the boundary of the box, but the value of the orientation RMSD is always within the error range ( the error added to the RDC data) indicating that the simulation is applying the rdc data correctly?Can someone explain to me why is this happening? or am i suppose to combine the 4 trajectories to view them together?I really appreciate any help or any extra tutorial that might help. Also if further details of the simulation needed please ask and ill ansewr.Thank youHanin Omar | | | | An introduction to replica exchange simulations: Mark Abraham, Session 1... | | | -- 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] Replica exchange question?
Hello all;i want to perform a REMD simulation with orientation restraint added, and i want to make sure that my scheme is correct so i have a few questions:1) if i have dihedral restraint or/and orientation restraint they should be added in all steps ( energy minimization, temperature coupling, pressure coupling and md production) right?2) when i do REMD, i perform temperature equiliberation for the different replicas at different temperature, following that i perform pressure equilibration at the same pressure values for all replica, then i run the replica exchange production, is that correct?3) is 500 exchange rate a good value for a 83 residue helical protein?4) i am confused, does REMD produces a different trajectory for each replica, because each replica has a slightly different md.log file? if so which replica should i consider the final best result?i really appreciate the helpHanin OMar -- 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] Grompp error
Hello everyone I am using gromacs version 2019, and I want to add dihedral restraint to the backbone of the last helix in my protein in my simulation, however grompp gives me this error ERROR 1 [file D2-TorisionRes.itp, line 5]: Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest. (after the function type). from my understanding this means that i am missing one feild in my restraint file, can someone tell me what is it?This is the content of my D2-TorisionRes.itp file :[ dihedral_restraints ] ;For the second domain starting from residue 74 ; ai aj ak al type label phi dphi kfac power ; C(i-1) Ni C-alphai Ci 1 1 value 0 1.0 2.0 1159 1174 1175 1176 1 1 -70.2 0 1.0 2.0 ;res 74 1176 1186 1187 1188 1 1 -91.0 0 1.0 2.0 ;res 75 1188 1205 1206 1207 1 1 -53.4 0 1.0 2.0 ;res 76 and in my topology file i added this line after the molecule:; Include Dihedral restraint file #ifdef DIHRE #include "D2-TorisionRes.itp" #endif and in my mdp file i used:define = -DDIHRE is my implementation of the dihedral restraint correct so far? also do i have to include them in all the equiliberation steps? THank you for the help Sent from my iPhone -- 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] NPT not working
Thank you Justin for your answer, i went back to my system and did all sort of tests, and the system works fine without the RDC restraint. Since the RDC values where used to generate the original pdb file of the protein i think the strongest option would be to say that i have an issue with the implementation of RDC constraints, so ill post how i implemented them and see if anyone cane pinpoint my mistakes:1) in the toplogy file: ; Include orientation restraint file ifdef POSRES #include "RDC-restraint.itp" endif 2) the RDC-restraint.itp had lines like these for 4 types of rdc (n-h , c-n, calpha-halpha, h-c): [ orientation_restraints ] ; ai aj type exp. label alpha const. obs. weight ; Hz nm^3 Hz Hz^-2 ; residue 1 5 6 1 1 1 3 -15.098 -15.0821 1 5 6 1 2 2 3 -15.098 10.8391 1 ; residue 2 18 20 1 1 3 3 1.53 -1.145444 1 18 20 1 2 4 3 1.53 -1.128506 1 20 21 1 1 5 3 6.083 7.72483 1 20 21 1 2 6 3 6.083 7.27571 1 18 21 1 1 7 3 -15.098 0.187741325 1 18 21 1 2 8 3 -15.098 3.13646 1 22 23 1 1 9 3 -15.098 -12.31345 1 22 23 1 2 10 3 -15.098 15.355 1 3) in the mdp file for the simulation: define = -DPOSRES ;use orientation restraint;Options for orientation restraint orire = yes orire-fc = 1 ; Orientation restraints force constant orire-tau = 0 ; Turn off time averaging orire-fitgrp = backbone is the problem with my implementation that they are using the rdc restraints for the water as well as the protein, and if so how can i specify that they should be fitted to just the protein?THank you for the answerHain On Thursday, November 1, 2018, 4:11:10 PM EDT, Justin Lemkul wrote: On 11/1/18 7:33 AM, Hanin Omar wrote: > Dear all gromacs user; > I am new to gromacs, and i desperatly need help. I want to use gromacs to > calculate the internal dynamics trajectory within a protein. > For my simulation i followed this protocol: > 1)Use pdb2gmx to generate the gro file and topology ( i chose amber99SB and > TIP3P water modrel) > 2)Energy minimization in vacuum > 3) set perodic boundery coditions > 4)solvate the system > 5) ADD ions to neutralize the system > 6)Energy minimization of the solvated system > 7) Position restrainted MD > 8)Unrestraind MD ( NVT equiliberation) > 9)Unrestraind MD ( NPT equiliberation) > 10)Run MD simulation with the addition of RDC restraint in the topology like > this > ; Include Position restraint file > #ifdef POSRES > #include "RDC-restraint.itp" > #endif > > The problem is i always get the following eroor when i run the last step > (Fatal error: > Error: Too many iterations in routine JACOBI) > I researched the error and some suggested that the system wasnt equiliberated > enough, after checking it seems that the NPT part doesn't converge, i tried > extending the time but that didnt solve it, i tired doing it in two steps: > 1st NPT with thermostat = v - rescale and barostat = Berendsen for say 6.5 ps > and then run 2ND NPT with thermostat = Nose-Hooover and barostat = Parinello > -Rahman for 6.5 ps.But that also didnt help. can someone explain why is this > happening( and if it has to do with the RDC constraints)? and how can i solve > it? If the introduction of RDC restraints causes a failure, then either (1) the implementation of the restraints is incorrect or (2) your structure is incompatible with those restraints, leading to the buildup of forces and a crash. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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.
[gmx-users] NPT not working
Dear all gromacs user; I am new to gromacs, and i desperatly need help. I want to use gromacs to calculate the internal dynamics trajectory within a protein. For my simulation i followed this protocol: 1)Use pdb2gmx to generate the gro file and topology ( i chose amber99SB and TIP3P water modrel) 2)Energy minimization in vacuum 3) set perodic boundery coditions 4)solvate the system 5) ADD ions to neutralize the system 6)Energy minimization of the solvated system 7) Position restrainted MD 8)Unrestraind MD ( NVT equiliberation) 9)Unrestraind MD ( NPT equiliberation) 10)Run MD simulation with the addition of RDC restraint in the topology like this ; Include Position restraint file #ifdef POSRES #include "RDC-restraint.itp" #endif The problem is i always get the following eroor when i run the last step (Fatal error: Error: Too many iterations in routine JACOBI) I researched the error and some suggested that the system wasnt equiliberated enough, after checking it seems that the NPT part doesn't converge, i tried extending the time but that didnt solve it, i tired doing it in two steps: 1st NPT with thermostat = v - rescale and barostat = Berendsen for say 6.5 ps and then run 2ND NPT with thermostat = Nose-Hooover and barostat = Parinello -Rahman for 6.5 ps.But that also didnt help. can someone explain why is this happening( and if it has to do with the RDC constraints)? and how can i solve it? THank you Hanin Omar Sent from my iPhone -- 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] No subject
Hello everybody, I am sending this email again to ask about orientation restraints in gromacs, in the manual it says that when writing the orientation restraints section in the topology file, one of the fields represent the constant c in the RDC equation, and the value for N-H vector are given as an example with the value of 6.083. Can someone tell me where I can retrieve this value for the other vectors ( N-H, H-H ... etc) or what are the values used in gromacs to calculate them? I really appreciate the help Thank you Hanin Omar Sent from my iPhone -- 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] How can I measure RDC fitness?
I am including orientation restraints in my md simulation for N-H vectors, how can I test RDC fitness to test if my simulation is actually doing what is expected of it? Thank you for your help Hanin Sent from my iPhone -- 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] help with orientation restraints
Hi all;I am an amateur gromacs user, but i have read all the tutorials i could find on how to perform md simulations using gromacs, however i still cant find any tutorial about how to include orientation restraints in my simulations. i want to perform a simulation on a helical protein and include 4 types of RDC data from two experiments. In the manual their is an example with N-H RDC data, however i need the constant ci for other types of RDC's ( C-N, C-H, Calpha-Halpha) does anybody know how to calculate them or where can i find them? also this is an example of the itp file that contains my RDC value:[ orientation_restraints ] ; ai aj type exp. label alpha const. obs. weight ; Hz nm^3 Hz Hz^-2 ;residue 2 20 21 1 1 1 3 6.083 7.72483 1.0 20 21 1 2 2 3 6.083 7.27571 1.0 ;residue 4 46 47 1 1 3 3 6.083 1.864475 1.0 46 47 1 2 4 3 6.083 -14.2043 1.0 ;residue 5 66 67 1 1 5 3 6.083 10.16845 1.0 66 67 1 2 6 3 6.083 -11.278 1.0 and in the topology file i added this: ; Include 1a1z protein topology #include "1a1z.itp" ; Include Orientation restraint file #ifdef POSRES #include "ocNH.itp" #endif and then in my mdp files for the minimization, equiliberation and md i have this: define = -DPOSRES ; restrain the protein are these steps correct ??thank you for your helpHanin Omar -- 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.
