Re: [gmx-users] NPT not working
On 11/14/18 6:07 AM, Hanin Omar wrote: 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 I don't know anything about these types of restraints, but it seems you have two different restraints for each pair of atoms, which sounds fishy to me. Try turning them on one at a time. -Justin 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.
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.
Re: [gmx-users] NPT not working
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.
[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.
