[gmx-users] convert gromacs formats and xyz
Hi, Is anybody known how to convert gromacs formats and xyz? If VMD or catdcd can do it ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/convert-gromacs-formats-and-xyz-tp5009793.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] DCD can not open file 'md_0_1.xtc' for reading
at linux --- ubantu: use: catdcd -o md_0_1.xyz md_0_1.xtc error: CatDCD 4.0 dcdplugin) unrecognized DCD header: dcdplugin) [0]: 1995 [1]: 1059782656 dcdplugin) [0]: 0x07cb [1]: 0x3f2b dcdplugin) read_dcdheader: corruption or unrecognized file structure Error: could not open file 'md_0_1.xtc' for reading. How to fix it ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/DCD-can-not-open-file-md-0-1-xtc-for-reading-tp5009795.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: DCD can not open file 'md_0_1.xtc' for reading
at redhat INUXAMD64 use: catdcd -o md_0_1.xyz md_0_1.xtc error: CatDCD 4.0 dcdplugin) unrecognized DCD header: dcdplugin) [0]: 1995 [1]: 1059782656 dcdplugin) [0]: 0x07cb [1]: 0x3f2b dcdplugin) read_dcdheader: corruption or unrecognized file structure Error: could not open file 'md_0_1.xtc' for reading. Something wrong in somewhere, where is it ? Thank you very much! maggin by the way, 1.Download catdcd-4.0b.tar.gz 2.tar -zxvf catdcd-4.0b.tar.gz 3. add path LINUXAMD64/bin/catdcd4.0 to .bash_profile 4. source .bash_profile 5. which catdcd ~/softwares/LINUXAMD64/bin/catdcd4.0/catdcd 6. cd LINUXAMD64/bin/catdcd4.0 7. ls catdcd md_0_1.xtc 8. catdcd -o md_0_1.xyz md_0_1.xtc error: CatDCD 4.0 dcdplugin) unrecognized DCD header: dcdplugin) [0]: 1995 [1]: 1059782656 dcdplugin) [0]: 0x07cb [1]: 0x3f2b dcdplugin) read_dcdheader: corruption or unrecognized file structure Error: could not open file 'md_0_1.xtc' for reading. -- View this message in context: http://gromacs.5086.x6.nabble.com/DCD-can-not-open-file-md-0-1-xtc-for-reading-tp5009795p5009796.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: DCD can not open file 'md_0_1.xtc' for reading
I use pdb to do test : catdcd -o 1dx0.gro 1dx0.pdb error: CatDCD 4.0 dcdplugin) unrecognized DCD header: dcdplugin) [0]: 1380273473 [1]: 538987346 dcdplugin) [0]: 0x52454d41 [1]: 0x20204b52 dcdplugin) read_dcdheader: corruption or unrecognized file structure Error: could not open file '1dx0.pdb' for reading. It seems catdcd can not work! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/DCD-can-not-open-file-md-0-1-xtc-for-reading-tp5009795p5009797.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_cluster
Hi, I have a qustion how to use g_cluster to judge convergence of the simulation of peptide ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-cluster-tp5009690.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g_cluster
hi, Justin I read the paper Daura(1999) and other papers: Ensemble-based convergence analysis of biomolecular trajectories(2006) Helix propensities of short peptide: Molecular dynamics versus bioinformatics (2003) Assessing equilibration and convergence in biomolecular simulation (2002) but it seems no clearly concrete answer how to operation to do convergence analysis based on cluster analysis. So, I still confused a quantitative justification for the simulations' convergence from g_cluster. Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-cluster-tp5009690p5009696.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] can extract edr and cpt of one frame?
Hi, I want extract one frame from NPT to run MD because for md need npt.gro and npt.cpt So, if can we extract cpt of one frame? and because I want to check if this frame at equilibration state, use g_energy -f npt.edr So, if can we extract edr of one frame? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/can-extract-edr-and-cpt-of-one-frame-tp5009322.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: NVT .gro for NPT
Hi, Tsjerk You asked me a good question. Ya, sometime it accords my imagination to tell if it right or not. That's not the correct way. Maybe it near boundary, like at the boundary of dangerous. So let me have such question. maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/NVT-gro-for-NPT-tp5009205p5009210.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: a snapshot of NVT
Hi,Tsjerk, Oh, that's it ! Thank you very much for your kind help! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/a-snapshot-of-NVT-tp5009206p5009211.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to check if one protein broke into fragments during MD?
Hi, all 1dx0.pdb during MD step at 19532ps are broken into 8 fragments, as VMD show about bovin19532.gro http://gromacs.5086.x6.nabble.com/file/n5009221/aa.jpg as picture shows that at the bottom the number of protein is 8 while when I use VMD to see md_0_1.gro the last structure of MD finished http://gromacs.5086.x6.nabble.com/file/n5009221/bb.jpg at the bottom the number of protein is 1 So, it seems from last structure it can not tell if is this protein broken. Is there anyway to check if protein is broken during MD? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/How-to-check-if-one-protein-broke-into-fragments-during-MD-tp5009221.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: How to check if one protein broke into fragments during MD?
Hi, Justin the structure of 19532ps shows as http://gromacs.5086.x6.nabble.com/file/n5009235/aa2.png the structure of md_0_1 shows as http://gromacs.5086.x6.nabble.com/file/n5009235/cc.png So, how can I fix the structure of 19532ps like md_0_1 ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/How-to-check-if-one-protein-broke-into-fragments-during-MD-tp5009221p5009235.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: How to check if one protein broke into fragments during MD?
Hi, Justin, use: trjconv -dump 19532 -pbc nojump -s md_0_1.tpr -f md_0_1.xtc get: http://gromacs.5086.x6.nabble.com/file/n5009238/dd.png Thank you veru much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/How-to-check-if-one-protein-broke-into-fragments-during-MD-tp5009221p5009238.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Gromacs 4.5.5
Hi, Alaina Before you install GMX4.5.5, did you install cmake-2.8.8 and fftw-3.3.2 ? maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Gromacs-4-5-5-tp5009198p5009203.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] NVT .gro for NPT
Hi, all I run a small peptide, and after NVT, I got the XXX.gro file like this, http://gromacs.5086.x6.nabble.com/file/n5009205/next6_gro.bmp because the peptide not at the center of box, I use this .gro to run NPT, if it reasonable? If it's not good, how can I avoid such phenomenon? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/NVT-gro-for-NPT-tp5009205.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] a snapshot of NVT
Hi, all When I run a small peptide at NVT stage, I get a snapshot like this: http://gromacs.5086.x6.nabble.com/file/n5009206/next6_gro2.bmp I am not sure if it right, and can I use it for NPT ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/a-snapshot-of-NVT-tp5009206.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] a snapshot of NVT
Hi, all When I run a small peptide at NVT stage, I get a snapshot like this: http://gromacs.5086.x6.nabble.com/file/n5009209/next6_gro2.bmp I am not sure if it right, and can I use it for NPT ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/a-snapshot-of-NVT-tp5009209.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] refcoord_scaling = com
at md stage, can we set refcoord_scaling = com as follows, ; Pressure coupling is on pcoupl = Parrinello-Rahman; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p= 2.0 ; time constant, in ps ref_p= 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling = com at lysozyme tutorial there is no refcoord_scaling set. I'm not sure if it could do that set refcoord_scaling = com at md stage Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/refcoord-scaling-com-tp5009141.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Steepest Descents in vacuo
Before do Steepest with water, we first do Steepest Descents in vacuo, if such way will better to only do Steepest with water ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Steepest-Descents-in-vacuo-tp5009143.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: distance_restraints
Hi, Tsjerk, I have one question that in what situation people do constraint ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009144.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: distance_restraints
Hi, Tsjerk, Oh, so that's it . Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009146.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: refcoord_scaling = com
Hi, Justin, At md step, protein run out of box, if it will better that set position constraint, let protein at center of box? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/refcoord-scaling-com-tp5009141p5009150.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Steepest Descents in vacuo
Hi, Justin, Thank you very much for your help! Another question is when we do steep minimization, if it will be better first do steep with constraint, then do steep without constraint? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Steepest-Descents-in-vacuo-tp5009143p5009152.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Steepest Descents in vacuo
Hi, Justin, If I use Pymol to set up a mutation of 1dx0.pdb, If it best do Steepest Descents in vacuo first ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Steepest-Descents-in-vacuo-tp5009143p5009153.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: distance_restraints
Hi, Justin, I use Pymol to align the NMR structure and the structure after steep minimization, find problematic areas are superposition very well, while all the problematic areas have same character, that after steep minimization, Amino acid will lose some H atoms connect with C http://gromacs.5086.x6.nabble.com/file/n5009124/GLY124.png http://gromacs.5086.x6.nabble.com/file/n5009124/PRO137.png http://gromacs.5086.x6.nabble.com/file/n5009124/PHE141.png http://gromacs.5086.x6.nabble.com/file/n5009124/ASP144.png http://gromacs.5086.x6.nabble.com/file/n5009124/PRO165.png http://gromacs.5086.x6.nabble.com/file/n5009124/VAL166.png When I check other place, find they are same with the problematic areas, amino acid lose some H atoms connect with C So, it's unlike lose H atomes cause these LINCS WARNING. maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009124.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: distance_restraints
Hi, Justin, It's seems no problem at steep energy minimization, except lose H atoms connect with C, the superposition are very well. When I use Pymol to align the NMR structure and the structure after cg minimization, because cg is after steep, so same as steep, they lose H atoms that connect with C. but superposition is not so good with steep. It seems have some distanc and angles between problematic areas, and also as to good areas. problematic areas: atom1 atom2 1 N1+ (GLY124 N) 4 H (GLY124 HT3) http://gromacs.5086.x6.nabble.com/file/n5009127/GLY124_cg.png atom1 atom2 181 C (PRO137 CD)182 H (PRO137 HD1) http://gromacs.5086.x6.nabble.com/file/n5009127/PRO137_cg.png atom1 atom2 262 H (PHE141 HD1) 263 C (PHE141 CE2) http://gromacs.5086.x6.nabble.com/file/n5009127/PHE141_cg.png atom1 atom2 296 O1-(ASP144 OD2) 297 C (ASP144 C) http://gromacs.5086.x6.nabble.com/file/n5009127/ASP144_cg.png atom1 atom2 685 O (PRO165 O) http://gromacs.5086.x6.nabble.com/file/n5009127/PRO165_cg.png atom1 atom2 685 O (PRO165 O) 688 C (VAL166 CA) http://gromacs.5086.x6.nabble.com/file/n5009127/VAL166_cg.png good area: PRO158 http://gromacs.5086.x6.nabble.com/file/n5009127/PRO158_cg.png analysis: 1) 1 N1+ (GLY124 N) 4 H (GLY124 HT3) because GLY124 is N-end, and have a positive charge, so after cg minimization, it move long range, so have LINCS WARNING 2)181 C (PRO137 CD)182 H (PRO137 HD1) because at steep minimization, it lose HD1, so at cg minimization, it also lost HD1, so actually they have no bond, 3) 262 H (PHE141 HD1) 263 C (PHE141 CE2) 296 O1-(ASP144 OD2) 297 C (ASP144 C) 685 O (PRO165 O) 688 C (VAL166 CA) It seems for this group, atoms are far away, they are not form bond, but it looks cg take they as bonds, so it cause LINCS WARNING At such situation, what is the best way to deal with these LINCS WARNINGS? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009127.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: distance_restraints
Hi, Tsjerk I want equlibration enough time, so set NVT time 10ns , but simulation collapse at 7ns, protein have 7 fragments. Before NVT, I just do one time of steep energy minimization. So, I want first use constraint do steep, cg in vacuum, then add water, do steep, cg with constraint, then again do steep, cg without constraint. I hope after such steps my system will not collapse again in the next NVT, NPT and MD. Good energy minimization will contribute to simulation a lot. maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009130.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: distance_restraints
Hi, Justin, You are right, I should first fix the bad geometry. I check 1dx0.pdb, and the problematic areas are: atom1 atom2 1 N1+ (GLY124 N) 4 H (GLY124 HT3) 181 C (PRO137 CD)182 H (PRO137 HD1) 262 H (PHE141 HD1) 263 C (PHE141 CE2) 296 O1-(ASP144 OD2) 297 C (ASP144 C) 685 O (PRO165 O) 688 C (VAL166 CA) for these atoms bonds that rotated more than 30 degrees 1dx0.pdb is get from NMR. So, for the initial structure , is there anyways to solve these LINCS WARNING ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009076.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] distance_restraints
Hi, all I use GMX4.5.5, GROMOS96 53a6 force field ro simulation 1dx0.pdb, I use two steps energy minimization (steep and cg ) in vacuum as follows: 1. pdb2gmx -f 1dx0.pdb -o xxx.gro -ignh -ter -water spce -ss -p xxx.top 2. editconf -f xxx.gro -o xxx.pdb -c -d 0.9 -bt cubic 3.grompp -f em.mdp -c xxx.pdb -p xxx.top -o xxx.tpr 4.mdrun -v -s xxx.tpr -nt 2 -deffnm em_xxx 5.grompp_d -f cg.mdp -c em_xxx.gro -p xxx.top -o xxx.tpr 6.mdrun_d -v -s xxx.tpr -nt 2 -deffnm cg_xxx steep is no problem, while cg have some warnings: Step 143, Epot=-1.190781e+04, Fnorm=3.680e+01, Fmax=7.027e+02 (atom 217) Step 144, Epot=-1.190936e+04, Fnorm=2.620e+01, Fmax=2.688e+02 (atom 217) Step 145, Epot=-1.191034e+04, Fnorm=2.618e+01, Fmax=2.276e+02 (atom 277) Step 146, Epot=-1.191235e+04, Fnorm=3.672e+01, Fmax=4.235e+02 (atom 277) Step 147, Epot=-1.192020e+04, Fnorm=6.482e+01, Fmax=8.288e+02 (atom 219) Step 148, Epot=-1.196346e+04, Fnorm=1.315e+02, Fmax=1.971e+03 (atom 378) Step -1, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000694, max 0.004189 (between atoms 296 and 297) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step -1, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.009008, max 0.056534 (between atoms 1 and 4) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 181182 31.30.1000 0.1000 0.1000 685688 37.80.1000 0.1051 0.1000 262263 41.00.1000 0.1000 0.1000 1 4 39.20.1000 0.1057 0.1000 Step 149, Epot=-1.197948e+04, Fnorm=1.069e+02, Fmax=1.271e+03 (atom 218) Step 150, Epot=-1.198617e+04, Fnorm=6.868e+01, Fmax=9.492e+02 (atom 218) Step 151, Epot=-1.199312e+04, Fnorm=6.069e+01, Fmax=8.678e+02 (atom 378) Step 152, Epot=-1.199645e+04, Fnorm=2.884e+01, Fmax=3.323e+02 (atom 378) Step 153, Epot=-1.199771e+04, Fnorm=2.482e+01, Fmax=2.873e+02 (atom 378) Step 154, Epot=-1.199942e+04, Fnorm=3.681e+01, Fmax=6.652e+02 (atom 378) Step 155, Epot=-1.200439e+04, Fnorm=7.122e+01, Fmax=1.091e+03 (atom 378) . . . . . Step 208, Epot=-1.231153e+04, Fnorm=2.409e+01, Fmax=2.882e+02 (atom 262) Step 209, Epot=-1.231272e+04, Fnorm=2.635e+01, Fmax=3.012e+02 (atom 261) Step 210, Epot=-1.231523e+04, Fnorm=3.957e+01, Fmax=7.031e+02 (atom 378) Step 211, Epot=-1.232519e+04, Fnorm=6.187e+01, Fmax=1.273e+03 (atom 378) Step -1, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.01, max 0.05 (between atoms 775 and 776) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 262263 30.30.1000 0.1000 0.1000 Step 212, Epot=-1.233691e+04, Fnorm=4.926e+01, Fmax=5.858e+02 (atom 378) Step 213, Epot=-1.234682e+04, Fnorm=8.846e+01, Fmax=1.130e+03 (atom 261) Step 214, Epot=-1.235149e+04, Fnorm=8.846e+01, Fmax=1.372e+03 (atom 262) writing lowest energy coordinates. Back Off! I just backed up em_cg_constrain_vacuum.gro to ./#em_cg_constrain_vacuum.gro.1# Polak-Ribiere Conjugate Gradients converged to Fmax 100 in 275 steps Potential Energy = -1.25808627767813e+04 Maximum force = 9.11707505025239e+01 on atom 757 Norm of force = 1.65933958355887e+01 I constraint h-bond in cg.mdp: title = bovin cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = h-bonds integrator = cg dt = 0.002; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing= 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 4 ewald_rtol= 1e-5 optimize_fft= yes emtol = 100 emstep = 0.001 ; Highest order in the expansion of the constraint coupling matrix lincs_order = 8 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 293 gen-seed = 173529 in order to fix warning, I use distance_restraints as follows: genrestr -f em_xxx.gro -o posre.itp -disre_dist 0.1 -disre_up2 1 acording to the posre.itp, revise xxx.top file, ; Include Position restraint file #ifdef POSRES #include posre.itp [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 1 4 1 0 2 0.0 0.19 1.19 1.0 181 182 1 0 2 0.0 0.19 1.19 1.0 262 263 1 0 2 0.0 0.19 1.19 1.0 296 297 1 0 2 0.0 0.19 1.19 1.0 353 354 1 0 2 0.0 0.23 1.23 1.0 512 516 1 1 2 0.0 0.24 1.24 1.0 685 688 1 0 2 0.0 0.19 1.19 1.0 775 776 1 0 2 0.0 0.20 1.20 1.0 994 995 1 2 2 0.0 0.24 1.24 1.0 #endif But things not changed, same warning How should I do to fix it? Thank you very much! maggin
[gmx-users] energ minimization: cg and I-bfgs
0.1572 0.1390 921923 31.50.1445 0.1442 0.1340 923927 31.40.1444 0.1447 0.1340 923924 42.00.1482 0.1496 0.1340 924926 36.90.1065 0.1080 0.1000 924925 37.30.1068 0.1082 0.1000 Step 9, time 0.018 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.004632, max 0.116116 (between atoms 923 and 924) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 921923 31.50.1445 0.1442 0.1340 923927 31.40.1444 0.1447 0.1340 923924 42.00.1482 0.1496 0.1340 924926 36.90.1065 0.1080 0.1000 924925 37.30.1068 0.1082 0.1000 Step= 10, Dmax= 2.1e-02 nm, Epot= -4.63786e+05 Fmax= 3.33273e+03, atom= 1112 Step= 12, Dmax= 1.3e-02 nm, Epot= -4.65368e+05 Fmax= 3.16597e+03, atom= 518 Step= 13, Dmax= 1.5e-02 nm, Epot= -4.66743e+05 Fmax= 4.18187e+03, atom= 1112 Step= 14, Dmax= 1.9e-02 nm, Epot= -4.68028e+05 Fmax= 4.61798e+03, atom= 518 Step= 15, Dmax= 2.2e-02 nm, Epot= -4.68799e+05 Fmax= 5.19261e+03, atom= 522 Step= 16, Dmax= 2.7e-02 nm, Epot= -4.68896e+05 Fmax= 5.79535e+03, atom= 518 Step= 18, Dmax= 1.6e-02 nm, Epot= -4.72864e+05 Fmax= 1.66650e+03, atom= 522 Step= 19, Dmax= 1.9e-02 nm, Epot= -4.72901e+05 Fmax= 5.83070e+03, atom= 584 Step= 20, Dmax= 2.3e-02 nm, Epot= -4.75581e+05 Fmax= 4.25066e+03, atom= 160 Step= 22, Dmax= 1.4e-02 nm, Epot= -4.77224e+05 Fmax= 3.08540e+03, atom= 160 Step= 24, Dmax= 8.3e-03 nm, Epot= -4.78336e+05 Fmax= 1.29199e+03, atom= 160 Step= 25, Dmax= 1.0e-02 nm, Epot= -4.79314e+05 Fmax= 3.73890e+03, atom= 160 Step= 26, Dmax= 1.2e-02 nm, Epot= -4.80459e+05 Fmax= 2.21770e+03, atom= 160 Step= 27, Dmax= 1.4e-02 nm, Epot= -4.80600e+05 Fmax= 4.68351e+03, atom= 160 Step= 28, Dmax= 1.7e-02 nm, Epot= -4.81834e+05 Fmax= 3.60914e+03, atom= 160 Step= 30, Dmax= 1.0e-02 nm, Epot= -4.82982e+05 Fmax= 1.80313e+03, atom= 160 Step= 31, Dmax= 1.2e-02 nm, Epot= -4.83315e+05 Fmax= 4.15172e+03, atom= 160 Step= 32, Dmax= 1.5e-02 nm, Epot= -4.84337e+05 Fmax= 3.19667e+03, atom= 160 Step= 34, Dmax= 8.9e-03 nm, Epot= -4.85244e+05 Fmax= 1.44565e+03, atom= 160 Step= 35, Dmax= 1.1e-02 nm, Epot= -4.85711e+05 Fmax= 3.89936e+03, atom= 160 Step= 36, Dmax= 1.3e-02 nm, Epot= -4.86652e+05 Fmax= 2.48984e+03, atom= 160 Step= 38, Dmax= 7.7e-03 nm, Epot= -4.87292e+05 Fmax= 1.57431e+03, atom= 160 Step= 39, Dmax= 9.3e-03 nm, Epot= -4.87783e+05 Fmax= 3.04757e+03, atom= 160 Step= 40, Dmax= 1.1e-02 nm, Epot= -4.88394e+05 Fmax= 2.62054e+03, atom= 160 Step= 41, Dmax= 1.3e-02 nm, Epot= -4.88589e+05 Fmax= 3.92708e+03, atom= 160 Step= 42, Dmax= 1.6e-02 nm, Epot= -4.89062e+05 Fmax= 3.94266e+03, atom= 160 Step= 44, Dmax= 9.6e-03 nm, Epot= -4.90116e+05 Fmax= 9.30801e+02, atom= 160 writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.1# result: Steepest Descents converged to Fmax 1000 in 45 steps Potential Energy = -4.9011588e+05 Maximum force = 9.3080109e+02 on atom 160 Norm of force = 7.3772133e+01 then I do I-bfgs, Low-Memory BFGS Minimizer converged to machine precision in 175 steps, but did not reach the requested Fmax 100. Potential Energy = -5.38089209528220e+05 Maximum force = 1.94381568185624e+06 on atom 10842 Norm of force = 1.61130387384634e+04 I chang emstep=0.005, result also not chang. the .mdp is title = bovin cpp = /usr/bin/cpp ; the c pre-processor define = -DFLEXIBLE constraints = all-bonds integrator = l-bfgs dt = 0.002; ps ! nsteps = 2000 nstlist = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing= 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ;Energy minimizing stuff ; emtol = 100.0 emstep =0.005 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 293 gen-seed = 173529 So, I have the question that why for cg, it take place fatal error? and another question for steep, if the result is reasonable? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/energ-minimization-cg-and-I-bfgs-tp5008882.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www
[gmx-users] Steepest LINCS WARNING
in 53 steps Potential Energy = -4.9292250e+05 Maximum force = 9.9413483e+02 on atom 159 Norm of force = 6.9268021e+01 There are 4 LINCS WARNING at : 1.Gly273-Ser277 2.Gln582-Gln585 3.Gly34-Gly38 4.Asn919-Asn920 They are all bonds that rotated more than 30 degrees my .mdp : title = bovin cpp = /usr/bin/cpp ; the c pre-processor define = -DFLEXIBLE constraints = all-bonds integrator = steep dt = 0.002; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.4 fourierspacing= 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-5 optimize_fft = yes ; ;Energy minimizing stuff ; emtol = 1000.0 emstep =0.01 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = No nsttcouple = -1 nh-chain-length = 10 ; Groups to couple separately tc-grps = ; Time constant (ps) and reference temperature (K) tau-t= ref-t= ; Pressure coupling Pcoupl = No Pcoupltype = Isotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 1 compressibility = ref-p= ; Scaling of reference coordinates, No, All or COM refcoord_scaling = No ; Random seed for Andersen thermostat andersen_seed= 815131 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 293 gen-seed = 173529 I known something wrong in my system, but I don't known where it is ? Could you help me to find it out? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Steepest-LINCS-WARNING-tp5008919.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Steepest LINCS WARNING
when I first run enery minimization in vacuum, then add water model, (I use GROMOS96 53a6 force field, and spce water model) EM in water model: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 2000 Step=0, Dmax= 5.0e-03 nm, Epot= -3.51690e+05 Fmax= 2.16580e+04, atom= 21005 Step=1, Dmax= 5.0e-03 nm, Epot= -3.60975e+05 Fmax= 1.24353e+04, atom= 3050 Step=2, Dmax= 6.0e-03 nm, Epot= -3.73328e+05 Fmax= 8.74189e+03, atom= 3050 Step=3, Dmax= 7.2e-03 nm, Epot= -3.85332e+05 Fmax= 5.54552e+03, atom= 3050 Step=4, Dmax= 8.6e-03 nm, Epot= -3.98300e+05 Fmax= 3.03988e+03, atom= 20120 Step=5, Dmax= 1.0e-02 nm, Epot= -4.13757e+05 Fmax= 1.75853e+03, atom= 29072 Step=6, Dmax= 1.2e-02 nm, Epot= -4.29896e+05 Fmax= 1.55053e+03, atom= 29072 Step=7, Dmax= 1.5e-02 nm, Epot= -4.42239e+05 Fmax= 1.28428e+03, atom= 29072 Step=8, Dmax= 1.8e-02 nm, Epot= -4.53744e+05 Fmax= 1.40998e+03, atom= 920 Step=9, Dmax= 2.1e-02 nm, Epot= -4.61547e+05 Fmax= 4.89215e+03, atom= 520 Step= 10, Dmax= 2.6e-02 nm, Epot= -4.63542e+05 Fmax= 5.75251e+03, atom= 516 Step= 11, Dmax= 3.1e-02 nm, Epot= -4.64658e+05 Fmax= 5.56526e+03, atom= 520 Step 12, time 0.024 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.004301, max 0.126066 (between atoms 512 and 516) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 512516 39.00.1472 0.1565 0.1390 514518 38.50.1467 0.1558 0.1390 516520 38.80.1472 0.1557 0.1390 518520 38.70.1471 0.1550 0.1390 511514 39.70.1466 0.1561 0.1390 511512 40.10.1470 0.1561 0.1390 Step= 13, Dmax= 1.9e-02 nm, Epot= -4.67377e+05 Fmax= 3.11093e+03, atom= 5116 Step= 15, Dmax= 1.1e-02 nm, Epot= -4.68747e+05 Fmax= 2.97283e+03, atom= 520 Step= 16, Dmax= 1.3e-02 nm, Epot= -4.70028e+05 Fmax= 3.63802e+03, atom= 516 Step= 17, Dmax= 1.6e-02 nm, Epot= -4.71166e+05 Fmax= 4.03533e+03, atom= 520 Step= 18, Dmax= 1.9e-02 nm, Epot= -4.71943e+05 Fmax= 4.96009e+03, atom= 516 Step= 19, Dmax= 2.3e-02 nm, Epot= -4.72558e+05 Fmax= 5.15705e+03, atom= 520 Step= 21, Dmax= 1.4e-02 nm, Epot= -4.75111e+05 Fmax= 1.55977e+03, atom= 511 Step= 22, Dmax= 1.7e-02 nm, Epot= -4.75363e+05 Fmax= 5.38247e+03, atom= 582 Step= 23, Dmax= 2.0e-02 nm, Epot= -4.77689e+05 Fmax= 3.75868e+03, atom= 159 Step= 25, Dmax= 1.2e-02 nm, Epot= -4.79001e+05 Fmax= 2.54107e+03, atom= 159 Step= 26, Dmax= 1.4e-02 nm, Epot= -4.79210e+05 Fmax= 4.39836e+03, atom= 159 Step= 27, Dmax= 1.7e-02 nm, Epot= -4.80268e+05 Fmax= 3.94950e+03, atom= 159 Step= 29, Dmax= 1.0e-02 nm, Epot= -4.81704e+05 Fmax= 1.36796e+03, atom= 159 Step= 30, Dmax= 1.2e-02 nm, Epot= -4.82183e+05 Fmax= 4.55734e+03, atom= 159 Step= 31, Dmax= 1.5e-02 nm, Epot= -4.83601e+05 Fmax= 2.65995e+03, atom= 159 Step= 33, Dmax= 8.9e-03 nm, Epot= -4.84347e+05 Fmax= 2.05512e+03, atom= 159 Step= 34, Dmax= 1.1e-02 nm, Epot= -4.84811e+05 Fmax= 3.30097e+03, atom= 159 Step= 35, Dmax= 1.3e-02 nm, Epot= -4.85461e+05 Fmax= 3.18540e+03, atom= 159 Step= 36, Dmax= 1.5e-02 nm, Epot= -4.85605e+05 Fmax= 4.31161e+03, atom= 159 Step= 37, Dmax= 1.9e-02 nm, Epot= -4.85983e+05 Fmax= 4.53453e+03, atom= 159 Step= 39, Dmax= 1.1e-02 nm, Epot= -4.87596e+05 Fmax= 1.03948e+03, atom= 366 Step= 40, Dmax= 1.3e-02 nm, Epot= -4.87792e+05 Fmax= 4.95272e+03, atom= 159 Step= 41, Dmax= 1.6e-02 nm, Epot= -4.89343e+05 Fmax= 2.61653e+03, atom= 159 Step= 43, Dmax= 9.6e-03 nm, Epot= -4.89881e+05 Fmax= 2.44528e+03, atom= 159 Step= 44, Dmax= 1.2e-02 nm, Epot= -4.90124e+05 Fmax= 3.33456e+03, atom= 159 Step= 45, Dmax= 1.4e-02 nm, Epot= -4.90496e+05 Fmax= 3.58399e+03, atom= 159 Step= 47, Dmax= 8.3e-03 nm, Epot= -4.91468e+05 Fmax= 6.25094e+02, atom= 366 writing lowest energy coordinates. Back Off! I just backed up em_constrain.gro to ./#em_constrain.gro.2# Steepest Descents converged to Fmax 1000 in 48 steps Potential Energy = -4.9146806e+05 Maximum force = 6.2509442e+02 on atom 366 Norm of force = 6.6710007e+01 LINCS WARNING relative constraint deviation after LINCS: rms 0.004301, max 0.126066 (between atoms 512 and 516) ATOM512 HD2 ARG A 156 -13.495 -6.447 -3.087 1.00 0.00 H ATOM516 NH1 ARG A 156 -14.923 -9.012 -5.069 1.00 0.00 N Befor EM in vacuum, there are 4 LINCS WARNING; now there are only one, But I have no idea what can I do, to kill this LINCS WARNING? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Steepest-LINCS-WARNING-tp5008919p5008920.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe
[gmx-users] cg Fatal error--DD cell
1)I use steepest to minimize energy, .mdp as follows, title = bovin cpp = /usr/bin/cpp ; the c pre-processor define = -DFLEXIBLE constraints = all-bonds integrator = steep dt = 0.002; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing= 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ;Energy minimizing stuff ; emtol = 1000.0 emstep =0.01 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 293 gen-seed = 173529 2) then I use cg do energy minimization, .mdp as follows, title = bovin cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = all-bonds integrator = cg dt = 0.002; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing= 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 4 ewald_rtol= 1e-5 optimize_fft= yes emtol = 100.0 emstep = 0.01 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 293 gen-seed = 173529 both constraint all bond, 1) steepest is no problem; but 2) some error take place at cg I use grompp_d -f em_cg_constrain.mdp -c em.pdb -p topol.top -o bovin_em_cg.tpr mdrun_d -v -s bovin_em_cg.tpr -deffnm em_cg Starting 16 threads, ... Fatal error: DD cell 1 4 0 could only obtain 14 of the 16 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. at em_cg.log , maximum distance required for P-LINCS: 0.876 nm So, I revised the mdrun, mdrun_d -v -s bovin_em_cg.tpr -deffnm em_cg -nt 2 -rcon 0.876 nm -dds 0.876 another error take place, Fatal error: Too many LINCS warnings (1011) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem So, is anyway to resolve it ? I have try, but can not find the way. Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/cg-Fatal-error-DD-cell-tp5008859.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: cg Fatal error--DD cell
the information on .log as follows: Initializing Domain Decomposition on 2 nodes Dynamic load balancing: no Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.598 nm, LJ-14, atoms 942 950 multi-body bonded interactions: 0.598 nm, Proper Dih., atoms 942 950 Minimum cell size due to bonded interactions: 0.657 nm User supplied maximum distance required for P-LINCS: 0.876 nm Using 0 separate PME nodes Optimizing the DD grid for 2 cells with a minimum initial size of 0.876 nm The maximum allowed number of cells is: X 7 Y 7 Z 7 Domain decomposition grid 2 x 1 x 1, separate PME nodes 0 PME domain decomposition: 2 x 1 x 1 Domain decomposition nodeid 0, coordinates 0 0 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Will do PME sum in reciprocal space. Anybody could tell me how to fix this problem! Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/cg-Fatal-error-DD-cell-tp5008859p5008875.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: how to add sodium acetate
Hi, Justin It's work ! Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/how-to-add-sodium-acetate-tp5008786p5008831.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] frame
Hi, if I run 20ns MD, and want to get the pdb at 19532ps trjconv -s md_0_1.tpr -f md_0_1.xtc -o bovin19532.gro -dt 1 -b 19532 -e 19532 editconf -f bovin19532.gro -o bovin19532.pdb If is it right? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-tp5008727.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: frame
How to convert ur frames in a time (ps)? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-and-pdb-tp5008727p5008735.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] frame in VMD
Hi, I use VMD to see GROMACS trajectory, I run 20ns md, there are 10,000,000 step, when load to VMD, it total 2777 frames. I don't known if there something wrong in it ? How to get the frame about 19532ps? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-in-VMD-tp5008737.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: frame
hi, Wagner It works! Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-and-pdb-tp5008727p5008768.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: FEP of ion binding protein
Hi, Steven, http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html and there is one paperGood Practices in Free-Energy Calculations J. Phys. Chem. B, 2010, 114 (32), pp 10235–10253 Hope this data could help you! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/FEP-of-ion-binding-protein-tp5008557p5008559.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g_hbond
Hi, Erik Thank you very much!Thank you! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507p5008548.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] tpr of extend simulation
Hi, I run MD production 10ns, and get file: md_0_1.trr, md_0_1.tpr but simulation time is not enough, so I extend the time to 20ns, tpbconv -s md_0_1.tpr -extend 1 -o md_0_1_next1.tpr and get file: traj.trr, md_0_1_next1.tpr trajectory cconnection : trjcat -f md_0_1.trr traj.trr -o traj_all_md.trr So, I have a question when I analysis trajectory use g_hbond g_hbond -f traj_all_md.trr -s md_0_1_next1.tpr -num bovin_hnum.xvg at here I use md_0_1_next1.tpr, if is it right ? I have some not sure Thank you! -- View this message in context: http://gromacs.5086.x6.nabble.com/tpr-of-extend-simulation-tp5008506.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond
# This file was created Fri May 24 13:03:14 2013 # by the following command: # g_hbond -f traj_all_md.trr -s md_0_1_next1.tpr -num bovin_hnum.xvg # # g_hbond is part of G R O M A C S: # # Green Red Orange Magenta Azure Cyan Skyblue # @title Hydrogen Bonds @xaxis label Time (ps) @yaxis label Number @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 74 517 2 73 515 4 69 515 6 69 529 8 78 525 10 74 517 12 68 516 14 68 524 16 71 520 hi, anybody can tell me at here if Hydrogen bonds Refers to the middle column: 74,73,69,69,78,74,68,68,71 Thank you ! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: NVT and NPT for small peptide
Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/NVT-and-NPT-for-small-peptide-tp5008461p5008508.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g_hbond
Hi, Pan Thank you very much for your kind help! Thank you! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507p5008513.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: residue labeling in g_rmsf
Hi, you can use Matlab software to do it! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/residue-labeling-in-g-rmsf-tp5008474p5008514.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Free energy of solvation's .mdp of peptide
Hi, if I want to calculate the free energy of solvation of peptide, because both van der Waals and Coulombic interactions are important for peptide so I set couple-lambda0 = none couple-lambda1 = vdw-q is it right? or it's better to choose wo-stage approach to do this work: van der Waals coupling: sc-alpha = 0.5 ; use soft-core for LJ (de)coupling sc-sigma = 0.3 sc-power = 1 couple-moltype= peptide couple-intramol = no couple-lambda0= none; non-interacting dummy in state A couple-lambda1= vdw ; only vdW terms on in state B Coulombic coupling: sc-alpha = 0 ; soft-core during (dis)charging can be unstable! sc-sigma = 0 couple-moltype= peptide couple-intramol = no couple-lambda0= vdw ; only vdW terms in state A (the previous state B is now A) couple-lambda1= vdw-q ; all nonbonded interactions are on in state B Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Free-energy-of-solvation-s-mdp-of-peptide-tp5008445.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] NVT and NPT for small peptide
Hi, when simulation small peptideS, 6 or 10 amino acid, how long it is need for NVT and NPT? -- View this message in context: http://gromacs.5086.x6.nabble.com/NVT-and-NPT-for-small-peptide-tp5008461.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Free energy of solvation about peptide
The BAR method calculates a ratio of weighted average of the Hamiltonian difference of state B given state A and vice versa. So, for different peptides, can this method apply to compare the stability of peptides? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/Free-energy-of-solvation-about-peptide-tp5008353p5008437.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Fatal error: Failed to lock: md.log. Function not implemented.
hi, Justin, Thank you very much! Thank you! Ya, it's works! great! cool! Thank you very much for your suggestion, this time I also not use -reprod ,it doesn't effect simulation. Work also can go on! Thank you very much for your kind help! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Fatal-error-Failed-to-lock-md-log-Function-not-implemented-tp500p5007800.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fatal error: Failed to lock: md.log. Function not implemented.
Hi, when I use GROMACS4.5.5 to do peptid simulation. At NVT step, system is not equilibration, so I extend NVT simulation as follows: tpbconv -s nvt.tpr -extend 2000 -o next1.tpr mpirun -np 4 mdrun_mpi -reprod -s next1.tpr -cpi nvt.cpt after finish this extending, I got files: traj.trr state_prev.cpt state.cpt md.log ener.edr confout.gro Though extending, this system is also not equilibration, so I continue extend: tpbconv -s next1.tpr -extend 1000 -o next2.tpr mpirun -np 4 mdrun_mpi -reprod -s next2.tpr -cpi state.cpt but it doesn't work, and get: Program mdrun_mpi, VERSION 4.5.5 Source code file: checkpoint.c, line: 1757 Fatal error: Failed to lock: md.log. Function not implemented. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors How could fix it? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Fatal-error-Failed-to-lock-md-log-Function-not-implemented-tp500.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
