[gmx-users] Box size problem
Dear All, I try to run a simulation with protein-membrane system in charmm36 ff with Gromacs5.0.4 and the simulation runs without complain.The problem is in the unit cell size which seems to grow during a short 500 ps simulation from ~15 to ~28 nm in Z direction although the system atoms remain confined in the~15 nm in Z direction. The GRO files before and after the 500 ps simulation can be downloaded from the following link: https://uni-muenster.sciebo.de/index.php/s/GBHjED2t1KzZZ2o And these are the MDP parameters used: MDP Parameters - integrator = md dt = 0.001 nsteps = 50 nstxout = 50 nstvout = 50 nstlog = 10 nstenergy = 50 nstxtcout = 50 xtc_grps= nstcalcenergy = 500 energygrps = ANA2 CHL1 POPC DOPC POPI POPS CAL cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 ; tcoupl = Nose-Hoover tc_grps = PROT MEMB SOL_ION tau_t = 1.01.01.0 ;ref_t = 303.15 303.15 303.15 ref_t = 200. 200. 200. ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; nstcomm = 100 comm_mode = linear comm_grps = PROT MEMB SOL_ION ; refcoord_scaling= com - No evident problem was displayed at TPRpreparation or MD run. Could some combination of parameters cause such a problem? With Gromacs 5.0.4 I have successfully simulated similar protein-membrane systemsin the past with the same charmm36 force field, but at that time different parameters I remember were suggested in Gromacs, particularly, the following ones: MDP Parameters (OLD) - integrator = md dt = 0.002 nsteps = 25000 nstxout = 50 nstvout = 50 nstlog = 10 nstenergy = 50 nstxtcout = 50 xtc_grps= energygrps = Protein CHL1 POPC DOPC POPS Water_and_ions ;energygrp_table= nstcalcenergy = 500 nstlist = 10 nstcomm = 50 comm_mode = Linear comm-grps = ns_type = grid rlist = 1.0 rlistlong = 1.4 rvdw_switch = 0.8 vdwtype = Switch coulombtype = pme rcoulomb= 1.0 rcoulomb_switch = 0.0 rvdw= 1.2 fourierspacing = 0.15 pme_order = 6 ;ewald_rtol = 1e-6 tcoupl = V-rescale ;nose-hoover nhchainlength = 1 tc-grps = Protein CHL1 POPC DOPC POPS Water_and_ions tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 ref_t = 293 293 293 293 293 293 Pcoupl = parrinello-rahman ;berendsen ;parrinello-rahman Pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 pbc = xyz gen_vel = no ;yes gen_temp= 293 optimize_fft= yes constraints = hbonds continuation= no constraint_algorithm = Lincs lincs-order = 4 ; 8 is needed for BD with large time-steps. lincs-iter = 1 ; 1 is fine for normal simulations, but use 2 to conserve energy in NVE runs. - In the new parameters I also tried to change the tcoupl from Nose-Hoover to V-rescale, but the outcome is the same, the box size becomes large. ProbablyI am missing something trivial. Does anybody have a clue what might be wrong? Thanks very much for any help. Davit -- 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] pdb2gmx fails on CHARMM36 terminal group
Just a small note about cholesterol CHL1 in the merged.rtp file of november 2016 release for CHARMM36 force field. The first four lines of CHL1 in merged.rtp: C3 CRL10.140 0 O3 OHL -0.660 1 H3' HOL0.430 2 H3 HGA10.090 3 While the sequence should be: C3 CRL10.140 0 H3 HGA10.090 3 O3 OHL -0.660 1 H3' HOL0.430 2 So that each hydrogen atom follow immediately the heavy atom. One could have this in mind for the next release? Thanks again. On 3/13/2017 6:41 PM, Davit Hakobyan wrote: Thank you very much! Indeed, it seems the problem was in the missing TER lines in combination with -chainsep for individual chain separation. Thank you again for all your kind help. Davit On 3/13/2017 6:21 PM, Justin Lemkul wrote: On 3/13/17 1:12 PM, Davit Hakobyan wrote: Thank you for the suggestion. I have tried to use the "-ter" flagbut this does not helpsince the problem is not because pdb2gmx cannot recognize the C-terminal patch, but that it misses the termianals of the intermediate proteins.The protein sequence in my system is like: ANAA,ANAC,P11A,P11C So even when I use the "-ter" flag the program asks to specify the N-termianl patch for ANAA and C-terminal patch for P11C. But all the four molecules are independent chains and each of them have both N-terminal (NH3+) and C-terminal (COO-). But pdb2gmx seems to treat them as a single long chain? You need to use TER between chains or assign them different chain identifiers in the PDB file, otherwise pdb2gmx assumes they're continuous. See -chainsep option. -Justin Thanks again for any help. Davit On 3/13/2017 5:54 PM, Mark Abraham wrote: Hi, pdb2gmx has options that configure its behaviour to let you choose whether PDB TER records and/or changes of chain ID should separate molecules, etc. You could explore those, and/or perhaps add such TER records to make your intent clearer to the tool. (But with incomplete information, I can't be sure that will help...) Mark On Mon, Mar 13, 2017 at 5:48 PM Davit Hakobyan <dhako...@uni-muenster.de> wrote: Dear All, I have a very big system with 4 proteins and membrane system. The relevant topology part is as follows: [ molecules ] ; Compound#mols ANAA 1 ANAC 1 P11A 1 P11C 1 CHL1 190 POPC 380 DOPC 190 POPI24 80 POPS 160 TIP3179172 SOD770 CLA351 CAL 30 The first four molecules are the proteins. Each of these molecules has CTER patch applied in CHARMM using charmm36 force field. During the convertion with pdb2gmx I get an error. Below are shown some relevant parts of the output: *Processing chain 1 (675703 atoms, 110937 residues)** **Identified residue MET1 as a starting terminus.** **Warning: Residue CHL11 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL12 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL13 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL14 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL15 in chain has different type (Other) from starting residue MET1 (Protein).** **More than 5 unidentified residues at end of chain - disabling further warnings.** **Identified residue LYS96 as a ending terminus.* Although there are warnings, however, the problem seems to be in another place. The next portion is the following: *Start terminus MET-1: NH3+** **End terminus LYS-96: COO-** **Opening force field file /home/d/dhako_01/bin/gromacs/share/gromacs/top/charmm36-nov2016.ff/merged.arn** * From the above one can see that the program only detected the CTER of the P11C molecule (it is 96 residues large) and missed the CTERS of ANAA, ANAC and P11A. And now comes the actual error: *Program gmx_5.0.4_mpi, VERSION 5.0.4** **Source code file: /home/d/dhako_01/src/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 732** ** **Fatal error:** **Atom OT1 in residue ASP 339 was not found in rtp entry ASP with 12 atoms** **while sorting atoms.** * I guess the above error indicates that the pdb2gmx could not detect the CTER portion of ANAA/ANAC (their last residue is ASP) so the error appears. Could someone suggest a resolution? Thanks a lot in advance. -- 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 s
Re: [gmx-users] pdb2gmx fails on CHARMM36 terminal group
Thank you very much! Indeed, it seems the problem was in the missing TER lines in combination with -chainsep for individual chain separation. Thank you again for all your kind help. Davit On 3/13/2017 6:21 PM, Justin Lemkul wrote: On 3/13/17 1:12 PM, Davit Hakobyan wrote: Thank you for the suggestion. I have tried to use the "-ter" flagbut this does not helpsince the problem is not because pdb2gmx cannot recognize the C-terminal patch, but that it misses the termianals of the intermediate proteins.The protein sequence in my system is like: ANAA,ANAC,P11A,P11C So even when I use the "-ter" flag the program asks to specify the N-termianl patch for ANAA and C-terminal patch for P11C. But all the four molecules are independent chains and each of them have both N-terminal (NH3+) and C-terminal (COO-). But pdb2gmx seems to treat them as a single long chain? You need to use TER between chains or assign them different chain identifiers in the PDB file, otherwise pdb2gmx assumes they're continuous. See -chainsep option. -Justin Thanks again for any help. Davit On 3/13/2017 5:54 PM, Mark Abraham wrote: Hi, pdb2gmx has options that configure its behaviour to let you choose whether PDB TER records and/or changes of chain ID should separate molecules, etc. You could explore those, and/or perhaps add such TER records to make your intent clearer to the tool. (But with incomplete information, I can't be sure that will help...) Mark On Mon, Mar 13, 2017 at 5:48 PM Davit Hakobyan <dhako...@uni-muenster.de> wrote: Dear All, I have a very big system with 4 proteins and membrane system. The relevant topology part is as follows: [ molecules ] ; Compound#mols ANAA 1 ANAC 1 P11A 1 P11C 1 CHL1 190 POPC 380 DOPC 190 POPI24 80 POPS 160 TIP3179172 SOD770 CLA351 CAL 30 The first four molecules are the proteins. Each of these molecules has CTER patch applied in CHARMM using charmm36 force field. During the convertion with pdb2gmx I get an error. Below are shown some relevant parts of the output: *Processing chain 1 (675703 atoms, 110937 residues)** **Identified residue MET1 as a starting terminus.** **Warning: Residue CHL11 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL12 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL13 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL14 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL15 in chain has different type (Other) from starting residue MET1 (Protein).** **More than 5 unidentified residues at end of chain - disabling further warnings.** **Identified residue LYS96 as a ending terminus.* Although there are warnings, however, the problem seems to be in another place. The next portion is the following: *Start terminus MET-1: NH3+** **End terminus LYS-96: COO-** **Opening force field file /home/d/dhako_01/bin/gromacs/share/gromacs/top/charmm36-nov2016.ff/merged.arn** * From the above one can see that the program only detected the CTER of the P11C molecule (it is 96 residues large) and missed the CTERS of ANAA, ANAC and P11A. And now comes the actual error: *Program gmx_5.0.4_mpi, VERSION 5.0.4** **Source code file: /home/d/dhako_01/src/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 732** ** **Fatal error:** **Atom OT1 in residue ASP 339 was not found in rtp entry ASP with 12 atoms** **while sorting atoms.** * I guess the above error indicates that the pdb2gmx could not detect the CTER portion of ANAA/ANAC (their last residue is ASP) so the error appears. Could someone suggest a resolution? Thanks a lot in advance. -- 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] pdb2gmx fails on CHARMM36 terminal group
Thank you. I have put the ZIP of the PDB file here: https://uni-muenster.sciebo.de/index.php/s/hO1OwfWMwwOy7xe The encountered error with the ASP residue relates to the C-terminal patch of the ANAA molecule which pdb2gmx missed and treating it as an unpatched ASP would give, of course, a mismatch error. Thanks a lot again for any suggestion. Davit On 3/13/2017 6:15 PM, Mark Abraham wrote: Hi, Using -ter to specify where molecules end won't help if there are not any TER records, but I can't tell what's in your file :-) Mark On Mon, Mar 13, 2017 at 6:12 PM Davit Hakobyan <dhako...@uni-muenster.de> wrote: Thank you for the suggestion. I have tried to use the "-ter" flagbut this does not helpsince the problem is not because pdb2gmx cannot recognize the C-terminal patch, but that it misses the termianals of the intermediate proteins.The protein sequence in my system is like: ANAA,ANAC,P11A,P11C So even when I use the "-ter" flag the program asks to specify the N-termianl patch for ANAA and C-terminal patch for P11C. But all the four molecules are independent chains and each of them have both N-terminal (NH3+) and C-terminal (COO-). But pdb2gmx seems to treat them as a single long chain? Thanks again for any help. Davit On 3/13/2017 5:54 PM, Mark Abraham wrote: Hi, pdb2gmx has options that configure its behaviour to let you choose whether PDB TER records and/or changes of chain ID should separate molecules, etc. You could explore those, and/or perhaps add such TER records to make your intent clearer to the tool. (But with incomplete information, I can't be sure that will help...) Mark On Mon, Mar 13, 2017 at 5:48 PM Davit Hakobyan <dhako...@uni-muenster.de wrote: Dear All, I have a very big system with 4 proteins and membrane system. The relevant topology part is as follows: [ molecules ] ; Compound#mols ANAA 1 ANAC 1 P11A 1 P11C 1 CHL1 190 POPC 380 DOPC 190 POPI24 80 POPS 160 TIP3179172 SOD770 CLA351 CAL 30 The first four molecules are the proteins. Each of these molecules has CTER patch applied in CHARMM using charmm36 force field. During the convertion with pdb2gmx I get an error. Below are shown some relevant parts of the output: *Processing chain 1 (675703 atoms, 110937 residues)** **Identified residue MET1 as a starting terminus.** **Warning: Residue CHL11 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL12 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL13 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL14 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL15 in chain has different type (Other) from starting residue MET1 (Protein).** **More than 5 unidentified residues at end of chain - disabling further warnings.** **Identified residue LYS96 as a ending terminus.* Although there are warnings, however, the problem seems to be in another place. The next portion is the following: *Start terminus MET-1: NH3+** **End terminus LYS-96: COO-** **Opening force field file /home/d/dhako_01/bin/gromacs/share/gromacs/top/charmm36-nov2016.ff/merged.arn** * From the above one can see that the program only detected the CTER of the P11C molecule (it is 96 residues large) and missed the CTERS of ANAA, ANAC and P11A. And now comes the actual error: *Program gmx_5.0.4_mpi, VERSION 5.0.4** **Source code file: /home/d/dhako_01/src/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 732** ** **Fatal error:** **Atom OT1 in residue ASP 339 was not found in rtp entry ASP with 12 atoms** **while sorting atoms.** * I guess the above error indicates that the pdb2gmx could not detect the CTER portion of ANAA/ANAC (their last residue is ASP) so the error appears. Could someone suggest a resolution? Thanks a lot in advance. -- 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 post
Re: [gmx-users] pdb2gmx fails on CHARMM36 terminal group
Thank you for the suggestion. I have tried to use the "-ter" flagbut this does not helpsince the problem is not because pdb2gmx cannot recognize the C-terminal patch, but that it misses the termianals of the intermediate proteins.The protein sequence in my system is like: ANAA,ANAC,P11A,P11C So even when I use the "-ter" flag the program asks to specify the N-termianl patch for ANAA and C-terminal patch for P11C. But all the four molecules are independent chains and each of them have both N-terminal (NH3+) and C-terminal (COO-). But pdb2gmx seems to treat them as a single long chain? Thanks again for any help. Davit On 3/13/2017 5:54 PM, Mark Abraham wrote: Hi, pdb2gmx has options that configure its behaviour to let you choose whether PDB TER records and/or changes of chain ID should separate molecules, etc. You could explore those, and/or perhaps add such TER records to make your intent clearer to the tool. (But with incomplete information, I can't be sure that will help...) Mark On Mon, Mar 13, 2017 at 5:48 PM Davit Hakobyan <dhako...@uni-muenster.de> wrote: Dear All, I have a very big system with 4 proteins and membrane system. The relevant topology part is as follows: [ molecules ] ; Compound#mols ANAA 1 ANAC 1 P11A 1 P11C 1 CHL1 190 POPC 380 DOPC 190 POPI24 80 POPS 160 TIP3179172 SOD770 CLA351 CAL 30 The first four molecules are the proteins. Each of these molecules has CTER patch applied in CHARMM using charmm36 force field. During the convertion with pdb2gmx I get an error. Below are shown some relevant parts of the output: *Processing chain 1 (675703 atoms, 110937 residues)** **Identified residue MET1 as a starting terminus.** **Warning: Residue CHL11 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL12 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL13 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL14 in chain has different type (Other) from starting residue MET1 (Protein).** **Warning: Residue CHL15 in chain has different type (Other) from starting residue MET1 (Protein).** **More than 5 unidentified residues at end of chain - disabling further warnings.** **Identified residue LYS96 as a ending terminus.* Although there are warnings, however, the problem seems to be in another place. The next portion is the following: *Start terminus MET-1: NH3+** **End terminus LYS-96: COO-** **Opening force field file /home/d/dhako_01/bin/gromacs/share/gromacs/top/charmm36-nov2016.ff/merged.arn** * From the above one can see that the program only detected the CTER of the P11C molecule (it is 96 residues large) and missed the CTERS of ANAA, ANAC and P11A. And now comes the actual error: *Program gmx_5.0.4_mpi, VERSION 5.0.4** **Source code file: /home/d/dhako_01/src/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 732** ** **Fatal error:** **Atom OT1 in residue ASP 339 was not found in rtp entry ASP with 12 atoms** **while sorting atoms.** * I guess the above error indicates that the pdb2gmx could not detect the CTER portion of ANAA/ANAC (their last residue is ASP) so the error appears. Could someone suggest a resolution? Thanks a lot in advance. -- 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] Is cholesterol model available in Charmm36 ff?
Dear All, A search for cholesterol model (cholesterol or CHL1 keywords) among the files of the CHARMM36 force field for Gromacs available at http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jan2014.ff.tgz; does not seem to give any result. Is the cholesterol model indeed still missing or is it present under a different name? Thanks very much in advance. -- 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.
