[gmx-users] How to find free energy barrier from FEL which generated from dPCA?
Dear Gromacs users, I have generated the FEL from dPCA of 20 residues length of peptide. I check the fel.txt file which was used for the FEL generation in mathmatica. I was not able to find the energy barriers from the FEL. I request you to guide to how to find the free energy barriers from this FEL. Thanks in Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to generate force field for carboxylated lysine residue?
Dear gromacs users Sorry for my previous email which has been sent by mistakenly. Coming to my problem, I have a protein which has carboxylated at N epsilon position of Lysine. I have gone through the many force fields and I did not find any force field which represents the carboxylated lysine. Then I got the topology file for carboxylated lysine ATB server. Now I have many questions in order to use this topology file. Firstly, how can I use this topology file. Do I need to add this topology file to the pdb2gmx force field? Secondly, can I add the atom types and other bonded and nonbonded information to existing force field files such .rtp, .atp and other files? Thirdly, do I need to add the geometry file my pdb file which is being simulated? Kindly tell me how handle with my carboxylated residue. Thanks in advane Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to generate force field for carboxylated lysine?
Dear gromacs users I have a protein which has carboxylated at N epsilon position of Lysine. I have gone through the many force fields and I did not find any force field which represents the carboxylated lysine. Then I got the topology file for carboxylated lysine ATB server. Now I have many questions in order to use this topology file. Firstly, how can I use this topology file. Do I need to add this topology file to the pdb2gmx force field? Secondly, can I add the atom types and other bonded and nonbonded information to existing force field files such .rtp, .atp and other files? Thirdly, do I need to add the geometry file my pdb file which is being simulated? I am lo Surya Graduate student India. -- 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] Can I take any conformational sub state from REMD
Dear gromacs users I have 20 residues length of peptide and it has some helix content. I have done REMD (with lower temperature range 300K and upper temperature 450K) to denature the helix. I gave desired exchange probability 0.25 and I got 30 temperature points and I did REMD simulations all 30 replicas. The helix is disappeared in the most of temperatures. Here my question comes. Can I take any conformational sub state from the REMD ensemble to do simulations with mutated residues? Thanks in advance Surya Graduate student India. -- 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] FEL generated by dPCA and radius of gyrationa vs RMSD
Dear gromacs users, I have generated free energy landscape by two methods such as dPCA and radius of gyration vs RMSD to average structure. In dPCA I got less number of meta conformational states than radius of gyration vs RMSD method. Can I use the second method for my paper submission? Thanks in advance Surya Graduate student India. -- 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] Methodology of dPCA
Dear gromacs users, I am Surya a Ph.D. scholar from lab of computational biology, CDFD, Hyderabad. I have done simulations for 100ns of 20 residue length peptide. I have done dPCA as mentioned in the gromacs tutorial. I have made a dangle.ndx file with all dihedral angles atom numbers. I created .trr file with 24 atoms of every time frame. Then based on the formula 2*N/3, I made another .ndx file of 24 atom numbers as my number of dihedral angles are 36 to create resized.gro file. Kindly tell me whether my methodology is correct to go ahead for further analysis such as gmx covar and gmx anaeig. Thanks in advance Surya Graduate student India. -- 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] I have not been able to do dPCA
Dear gromacs users, I would like to do dihedral PCA for my 20 residues trajectory. As I have interested in first 10 residues of my peptide, I have generated the .ndx file which has the dihedral atoms of first ten residues. Then I executed the following command. gmx_mpi angle -f md_0_1.xtc -s md_0_1.tpr -n dangle.ndx -or dangle.trr -type dihedral Here I got the two output files. Among them, one is dangle.trr which has only 14 atom positions with cos/sin. But I want ten residues atom positions cos/sin. In other words, I need to get for first ten residues atom positions cos/sin. I couldn't successful when I follow the dPCA tutorial on the gromacs site. Kindly tell me how to do it. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to use fastpca?
Dear gromacs users, I have installed fastpca to do the dihedral principal component analysis. But I am not getting how to use the fastpca. If anybody used this tool to do dPCA, let me know how to do it. Thanks in advance Surya Graduate student India. -- 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] Regarding DPCA
> Dear gromacs users > > I done simulations of peptide of 20 residues length for 300ns. As I would > like to explore the conformational flexibility I have chosen to do dPCA. I > have gone through the tutorial which is present in the gromacs cite. > Firstly, I have created the index file which shows the dihedral angle atom > numbers. I have given the 36 dihedral angles information of 18 residues. > Based on the formula 2*N/3 for 24 atoms I can create index file which can > be used in the neat step to create the .gro file. In my index file I gave > first 24 backbone atoms numbers. When use the gmx trjconv for getting > resized.gro I got following error. > > Fatal error: > Index[4] 25 is larger than the number of atoms in the > trajectory file (24). There is a mismatch in the contents > of your -f, -s and/or -n files. > > I got error meaning. In my index file fifth element is 25 which is greater > than the total number of atoms number that is 24. If I give first 24 > numbers Then I got .gro file only for first file as follow. > > Generated by trjconv : Protein in water t= 0.0 > 24 > 1LYS N1 -0.370 -0.929 0.912 > 1LYS H12 0.411 0.167 -0.986 > 1LYS H23 -0.533 0.846 -0.352 > 1LYS H34 -0.936 -0.603 0.798 > 1LYS CA5 0.049 -0.999 -1.000 > 1LYS HA6 -0.003 0.264 -0.965 > 1LYS CB7 0.935 -0.356 0.188 > 1LYSHB18 -0.982 0.862 -0.506 > 1LYSHB29 0.358 -0.934 0.839 > 1LYS CG 10 -0.544 0.010 -1.000 > 1LYSHG1 11 -0.646 0.763 -0.335 > 1LYSHG2 12 -0.942 -0.930 -0.367 > 1LYS CD 13 0.374 -0.927 -0.662 > 1LYSHD1 14 0.750 0.341 -0.940 > 1LYSHD2 15 -0.661 0.751 -0.775 > 1LYS CE 16 -0.632 -0.591 0.807 > 1LYSHE1 17 -0.561 0.828 0.693 > 1LYSHE2 18 0.721 0.610 -0.793 > 1LYS NZ 19 -0.410 0.912 -0.585 > 1LYSHZ1 20 -0.811 -0.419 0.908 > 1LYSHZ2 21 0.054 -0.999 -0.159 > 1LYSHZ3 22 0.987 0.203 -0.979 > 1LYS C 23 0.749 -0.663 -0.820 > 1LYS O 24 -0.573 -0.900 0.436 > 2.0 2.0 2.0 > > But I want to get the information for first 10 residues of my peptide. > Kindly tell me how to do get dPCA for first ten residues of my 20 residues > simulated peptide. It seems you only saved the first residue in your trajectory. If you make matching trajectory and .tpr files that save the first ten residues, then you should be able to proceed. -Justin Dear Justin In brief I would like to tell you my problem. I have taken the atom numbers those represent the dihedral angle atoms from the topology file to generate the index file to generate .trr file. Then I have generated the another index file for .gro file. As number of dihedral angles 36 for 18 residues, I could save 24 atoms according to 2*N/3 formula. As my area of interest is first 2-12 residues, I have taken numbers of backbone atoms in my index file for resized.gro file. Then I executed the following command trjconv -s foo.tpr -f dangle.trr -o resized.gro -n covar.ndx -e 0 Here I got the error as follow > Fatal error: > Index[4] 25 is larger than the number of atoms in the trajectory file (24). There is a mismatch in the contents of your -f, -s and/or -n files. Now come to your suggestion, you suggested me that first make matching trajectory and .tpr files for 10 residues. Here I not able to getting how does that work. Because we have to generate the .trr file based on the dihedral index file, which means definitely I will get the same error. Kindly tell me more about how to generate the resized.gro file for first 10 residues. Thanks in advance Surya Graduate student India. -- 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] cannot successfully finished the dPCA
Dear gromacs users I done simulations of peptide of 20 residues length for 300ns. As I would like to explore the conformational flexibility I have chosen to do dPCA. I have gone through the tutorial which is present in the gromacs cite. Firstly, I have created the index file which shows the dihedral angle atom numbers. I have given the 36 dihedral angles information of 18 residues. Based on the formula 2*N/3 for 24 atoms I can create index file which can be used in the neat step to create the .gro file. In my index file I gave first 24 backbone atoms numbers. When use the gmx trjconv for getting resized.gro I got following error. Fatal error: Index[4] 25 is larger than the number of atoms in the trajectory file (24). There is a mismatch in the contents of your -f, -s and/or -n files. I got error meaning. In my index file fifth element is 25 which is greater than the total number of atoms number that is 24. If I give first 24 numbers Then I got .gro file only for first file as follow. Generated by trjconv : Protein in water t= 0.0 24 1LYS N1 -0.370 -0.929 0.912 1LYS H12 0.411 0.167 -0.986 1LYS H23 -0.533 0.846 -0.352 1LYS H34 -0.936 -0.603 0.798 1LYS CA5 0.049 -0.999 -1.000 1LYS HA6 -0.003 0.264 -0.965 1LYS CB7 0.935 -0.356 0.188 1LYSHB18 -0.982 0.862 -0.506 1LYSHB29 0.358 -0.934 0.839 1LYS CG 10 -0.544 0.010 -1.000 1LYSHG1 11 -0.646 0.763 -0.335 1LYSHG2 12 -0.942 -0.930 -0.367 1LYS CD 13 0.374 -0.927 -0.662 1LYSHD1 14 0.750 0.341 -0.940 1LYSHD2 15 -0.661 0.751 -0.775 1LYS CE 16 -0.632 -0.591 0.807 1LYSHE1 17 -0.561 0.828 0.693 1LYSHE2 18 0.721 0.610 -0.793 1LYS NZ 19 -0.410 0.912 -0.585 1LYSHZ1 20 -0.811 -0.419 0.908 1LYSHZ2 21 0.054 -0.999 -0.159 1LYSHZ3 22 0.987 0.203 -0.979 1LYS C 23 0.749 -0.663 -0.820 1LYS O 24 -0.573 -0.900 0.436 2.0 2.0 2.0 But I want to get the information for first 10 residues of my peptide. Kindly tell me how to do get dPCA for first ten residues of my 20 residues simulated peptide. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to do dPCA
Dear gromacs users, I have done simulations of 20 residues length peptide for 300ns. As I would like to do explore the conformational space I have chosen the dPCA to find flexible regions. I have gone through the dPCA tutorial from gromacs site and followed it. First I have generated the index file by mk_angndk and I got following index file and I have chosen zero group (top one). [ Phi=180.0_2_43.93 ] 52523242747454649696768 7188868790999798 101 121 119 120 123 131 129 130 133 143 141 142 135 139 138 140 145 162 160 161 164 169 167 168 171 179 177 178 180 193 191 192 195 204 202 203 206 211 209 210 213 231 229 230 233 253 251 252 255 270 268 269 272 286 284 285 288 297 295 296 299 313 312 314 [ Phi=180.0_2_4.18 ] 232725264549474867716970 8690888997 10199 100 119 123 121 122 129 133 131 132 141 145 143 144 160 164 162 163 167 171 169 170 177 180 179 188 191 195 193 194 202 206 204 205 209 213 211 212 229 233 231 232 251 255 253 254 264 262 266 267 268 272 270 271 284 288 286 287 295 299 297 298 308 306 310 311 [ Phi=180.0_2_4.60 ] 215 218 221 219 218 223 219 220 218 225 221 222 219 227 223 224 221 227 225 226 223 225 227 228 257 260 262 261 260 266 262 263 261 266 264 265 301 304 306 305 304 310 306 307 305 310 308 309 Then I have to get another index file which tells to the trjconv to generate .gro file. Here I am unable to generate index file. As I want to create complete peptide .gro file except both terminal residues. Based on the 2*N/3 formula, it is not possible to create complete .gro file. Kindly tell how to create complete gro file for peptide of my interest. Thanks in advance Surya Graduate student India. -- 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] unable to understand dPCA
Dear gromacs users, I have done simulations of 20 residues length peptide for 300ns. As I would like to do explore the conformational space I have chosen the dPCA to find flexible regions. I have gone through the dPCA tutorial from gromacs site and followed it. First I have generated the index file by mk_angndk and I got following index file and I have chosen zero group (top one). [ Phi=180.0_2_43.93 ] 52523242747454649696768 7188868790999798 101 121 119 120 123 131 129 130 133 143 141 142 135 139 138 140 145 162 160 161 164 169 167 168 171 179 177 178 180 193 191 192 195 204 202 203 206 211 209 210 213 231 229 230 233 253 251 252 255 270 268 269 272 286 284 285 288 297 295 296 299 313 312 314 [ Phi=180.0_2_4.18 ] 232725264549474867716970 8690888997 10199 100 119 123 121 122 129 133 131 132 141 145 143 144 160 164 162 163 167 171 169 170 177 180 179 188 191 195 193 194 202 206 204 205 209 213 211 212 229 233 231 232 251 255 253 254 264 262 266 267 268 272 270 271 284 288 286 287 295 299 297 298 308 306 310 311 [ Phi=180.0_2_4.60 ] 215 218 221 219 218 223 219 220 218 225 221 222 219 227 223 224 221 227 225 226 223 225 227 228 257 260 262 261 260 266 262 263 261 266 264 265 301 304 306 305 304 310 306 307 305 310 308 309 Then I have to get another index file which tells to the trjconv to generate .gro file. Here I am unable to generate index file. As I want create complete complete peptide .gro file except both terminal residues. Based on the 2*N/3 formula, it is not possible to create complete .gro file. Kindly tell how to create complete gro file for peptide of my interest. Thanks in advance Surya Graduate student India. -- 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] Hydrogen bonds for particular residue during simulations.
Dear gromacs users, I have done simulations of 20 residue length of peptide for 100ns. I want to find hydrogen bonds for residue GLU-7. The topology information for this residue as follow. ; residue 7 GLU rtp GLU q -1.0 121 opls_238 7GLU N 39 -0.514.0067 ; qtot 4.5 122 opls_241 7GLU H 390.3 1.008 ; qtot 4.8 123 opls_224B 7GLU CA 39 0.14 12.011 ; qtot 4.94 124 opls_140 7GLU HA 39 0.06 1.008 ; qtot 5 125 opls_136 7GLU CB 40 -0.12 12.011 ; qtot 4.88 126 opls_140 7GLUHB1 40 0.06 1.008 ; qtot 4.94 127 opls_140 7GLUHB2 40 0.06 1.008 ; qtot 5 128 opls_274 7GLU CG 41 -0.22 12.011 ; qtot 4.78 129 opls_140 7GLUHG1 41 0.06 1.008 ; qtot 4.84 130 opls_140 7GLUHG2 41 0.06 1.008 ; qtot 4.9 131 opls_271 7GLU CD 420.7 12.011 ; qtot 5.6 132 opls_272 7GLUOE1 42 -0.815.9994 ; qtot 4.8 133 opls_272 7GLUOE2 42 -0.815.9994 ; qtot 4 134 opls_235 7GLU C 430.5 12.011 ; qtot 4.5 135 opls_236 7GLU O 43 -0.515.9994 ; qtot 4 Kindly suggest me how to create index file for this residue. Thanks in advance Surya Graduate student India. -- 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] water molecule cannot be settled during minimization!!!!
Dear gromacs users I am trying to simulate one protein with 180 residues. During energy minimization I got the falling error. Fatal error: step 26: Water molecule starting at atom 28787 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. I have reduced the em step size from 0.01 to 0.02 as I got this suggestion from archives. I still have the same problem. I request you to give a suggestion how to resolve it. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to do neutralization?
Dear gromacs users I got the system non-zero total charge: -0.226000. When I add one NA ion to the system I got non-zero total charge: +0.77. What is the way to neutralize the system? Thanks in advance Surya Graduate student India. -- 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] force field for selinomethionine?
Dear gromacs users, I have to do simulations for a peptide which has the selinomethionine. But regular force fields from gromacs has no information for this residue. kindly give me information if is there any force field for selinometheoinine. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to do dPCA?
Dear gromacs users I would like to do dPCA for my 100ns trajectory. When see in the gromacs tutorial I could not create the covar.ndx file. My peptide is 20 residues length. I made .ndx file for dihedral angles and after generating the dangle.trr file. But here I have one problem, to generate the .gro file we have to create the covar.ndx file based on the 2*N/3 formula. As my peptide has 20 dihedral angles, the covar.ndx file will have 14 atoms. But I want to generate .gro file to my complete peptide (20 residues). I request you to here help me out. Thanks in advance Surya Graduate student India. -- 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] Whether my simulation is conserved?
Dear gromacs users, I have done simulations for 100ns. To know whether my simulation is conserved, I have preferred to do simulated annealing. I have set the highest temperature as 350K at 25ns and allowed it go down to room temperature 300K at 50ns. And eventually I executed the mdrun for 50ns at 300K(you can find SA parameters below). From this simulated annealing trajectory how can I find global minima of protein? ;simulated annealing annealing = single single annealing-npoints = 3 3 annealing-time = 0 25000 5 0 25000 5 annealing-temp = 300 350 300 300 350 300 Surya Graduate student India. -- 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] successive removal of position restrain?
Dear gromacs users, I have gone through one gromacs tutorial of md simulation in solvent. Where they mentioned that successive removal of position restrain. In other words first they have done NPT ensemble with 1000 1000 1000 energy constants, then re executed the NPT ensemble with 100 100 100 energy constants and finally third time they ran the NPT ensemble with 10 10 10 energy constants. After this run they have stated the real MD production run with position restraint. But I have done NPT ensemble only with 1000 1000 1000 force constant and then I removed the complete position restrains before MD production run. My question comes here, Is there any difference between their methodology and my methodology? Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Error in simulated annealing
Dear gromacs users, I wanted to do simulated annealing and I set up the .mdp file as follow... title = OPLS 4qam MD simulation define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5000 = 50 ps (100 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 5 ; save coordinates every 100.0 ps nstvout = 5 ; save velocities every 100.0 ps nstenergy = 5 ; save energies every 100.0 ps nstlog = 5 ; update log file every 100.0 ps nstxout-compressed = 5 ; save compressed coordinates every 100.0 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System; replaces xtc-grps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm= lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet scheme rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; 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 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off *;simulated annealingannealing= single periodicannealing-npoints = 4 3annealing-time= 0 4000 8000 12000 16000 2 24000annealing-temp = 300 310 315 330 320 310 300* when I executed the mdrun with above .mdp file I got following error. *Fatal error:First time point for annealing > init_t. * Kindly tell me what could be the reason for the error. Thanks in advance *,* Surya Graduate student India. -- 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] Setting up SA
Dear gromacs users, I have one peptide which has 25 residues. I have done simulation for 100ns. When I presented my analysis in lab, I was suggested to do investigation of my simulation by simulated annealing (SA). Then I have gone through the simulated annealing notes which I found on gromacs website and I got some idea to do simulated annealing. I added the annealing points and temperatures in my .mdp file as follow. ;simulated annealing annealing= single annealing-points = 7 annealing-time= 0 4000 8000 12000 16000 2 24000 annealing-temp = 300 310 315 330 320 310 300 What I want to do here is that first try to increase the temperature gradually for some time then get it down to the reference temperature i.e 300K and allowed it to end of the simulation (100ns). Kindly tell me whether my simulated annealing set up is correct. Surya Graduate student India. -- 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] Simulated annealing
Dear gromacs users, I am extremely sorry for my previous incomplete mail. By mistaken I have pressed some short cut key. I have one peptide which has 25 residues. I have done simulation for 100ns. When I presented my analysis in lab, I was suggested to do investigation of my simulation by simulated annealing. Then I have gone through the simulated annealing notes which I found on gromacs website and I got some idea to do simulated annealing. I added the annealing points and temperatures in my .mdp file as follow. ;simulated annealing annealing= single annealing-points = 7 annealing-time= 0 4000 8000 12000 16000 2 24000 annealing-temp = 300 310 315 330 320 310 300 What I want to do here is that first try to increase the temperature gradually for some time then get it down to the reference temperature i.e 300K and allowed it to end of the simulation (100ns). Kindly tell me whether my simulated annealing set up is correct. Thanks in advance Surya Graduate student India. -- 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] setting up simulated annealing
Dear gromacs users, I have one peptide which has 25 residues. I have done simulation for 100ns. When I presented my analysis in lab, I was suggested to do investigation of my simulation by simulated annealing. Then I have gone through the simulated annealing notes which I found on gromacs website and I got some idea to do simulated annealing. I added the annealing points and temperatures in my .mdp file as follow. ;simulated annealing annealing Surya Graduate student India. -- 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] evaluation of simulated frames by procheck
Dear gromacs users, I have done simulation of peptide with 28 residues length for 100ns. I have used the OPLS force field. My peptide is disordered peptide and two of its regions have been modeled by using modellar. After modelling I have checked the steriochemical properties of the peptide by procheck and their G-factor value is greater than -0.5. After my simulations I have taken some of the frames randomly and checked the steriochemical properties of them by procheck and I got G-factor value is less than -0.5. If the G-factor value less than the reference value i.e -0.5 the structure has to be validated. I got less G-factor values for my all frames. Now my question comes here. As I didn't get greater G-factor values than reference values, is my simulation not valid? For your information all ramachandran angles are in allowed regions. And also suggest how to defend my simulation is valid. Thanks in advance Surya Graduate student India. -- 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] Has omega -180 also in proteins?
Dear gromacs users, I have done simulation for 100ns and I analyzed many properties as part of my work. I also calculated the omega dihedral angle and I got the values around +180 and -180 degrees. When I present the work in lab they questioned about the omega values of PROLINE. It should be around +180(trans) degrees, 0 (cis) degrees. But I got omega values around -180 degrees for PRO. Kindly tell me whether I am wrong. I have used gmx chi for my analysis. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to get omega angles for a trajectory?
Dear gromacs users, I would like to compute omega angles for a trajectory which I have simulated. when I use "gmx chi" command I got some 5 column data with S1 S2 para meters. I didn't understand that data. Kindly tell me how do I get omega angles for trajectory? Thanks in advance Surya Graduate student India. -- 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] Doubt in RMSD
> Dear gromacs users, >> >> I have done simulations for 100ns. My peptide length is 25 residue length. >> While calculating the RMSD by executing the gmx rms I have used 2 C-alpha >> atoms at N-terminal and one C-alpha atom at C-terminal for least square >> fitting and then calculated the RMSD for the rest of the C-alpha atoms. >> Among the frames some frames got more than 2nm RMSD with respect to >> starting structure. I have doubt here. 2nm means (20 Angstrom) is very >> high, is it possible to get this mush deviation with respect to starting >> structure? If it is yes, what is the reason for deviation? >> > > Have you watched the trajectory to see what happens? Such a short peptide > may simply unfold and the RMSD would be reasonable in that case. > > -Justin > > > Dear Justin, > > The topology of the peptide is like thread, in other words the peptide is > already unfolded (it is intrinsically disordered region). while doing > simulations I have fixed the end residues. I have watched the trajectory in > VMD. And there is no problem in trajectory. > If it's an IDP then RMSD can be quite high as the structural has considerable plasticity. RMSD is a degenerate metric; it doesn't tell you much about systems like these. -Justin Dear Justin, I have one more doubt regarding RMSD. I have executed the following command to calculate the RMSD. gmx rms -s 1kr1.tpr -f 1kr1_noPBC.xtc -n index.ndx -tu ns -o rmsd.xvg and I plotted the rmsd by xmgrace. As mentioned earlier I got more than 2nm for some frames in the trajectory with respect to the starting structure. When calculated the RMSD for one of the 2nm frame by using vmd or pymol I got around 2nm of RMSD. But when I align (superimposition) one of the 2nm RMSD frame with starting structure and If I checked RMSD, it is around 1nm. My doubt comes here, while executing the above command whether gmx rms consider the superimposition? Thanks in advance Surya Graduate student India. -- 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] Doubt in RMSD
Dear gromacs users, > > I have done simulations for 100ns. My peptide length is 25 residue length. > While calculating the RMSD by executing the gmx rms I have used 2 C-alpha > atoms at N-terminal and one C-alpha atom at C-terminal for least square > fitting and then calculated the RMSD for the rest of the C-alpha atoms. > Among the frames some frames got more than 2nm RMSD with respect to > starting structure. I have doubt here. 2nm means (20 Angstrom) is very > high, is it possible to get this mush deviation with respect to starting > structure? If it is yes, what is the reason for deviation? > Have you watched the trajectory to see what happens? Such a short peptide may simply unfold and the RMSD would be reasonable in that case. -Justin Dear Justin, The topology of the peptide is like thread, in other words the peptide is already unfolded (it is intrinsically disordered region). while doing simulations I have fixed the end residues. I have watched the trajectory in VMD. And there is no problem in trajectory. Surya Graduate student India. -- 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] doubt in RMSD
Dear gromacs users, I have done simulations for 100ns. My peptide length is 25 residue length. While calculating the RMSD by executing the gmx rms I have used 2 C-alpha atoms at N-terminal and one C-alpha atom at C-terminal for least square fitting and then calculated the RMSD for the rest of the C-alpha atoms. Among the frames some frames got more than 2nm RMSD with respect to starting structure. I have doubt here. 2nm means (20 Angstrom) is very high, is it possible to get this mush deviation with respect to starting structure? If it is yes, what is the reason for deviation? Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to find free energy barriers between conformational sub-states of simulation?
Dear gromacs users, I have done simulations of 20 residue length peptide for 100ns. I have performed clustering and got some 29 clusters. Now would like to calculate the free energy difference between these clusters. kindly tell me how to find the free energy difference between the clusters. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to resolve OXT atom issue?
Dear Justin, I apologize you as I am wasting your valuable time. I have peptide with 69 residues and some of the SER and THR residues are phosphorylated and also some of the missing residues(1 to 6; 36 to 41 and 69) have been modeled by modeller . I have chosen charmm36 force field. When I executed the command pdb2gmx -f 1th1.pdb -o 1th1_processed.gro -water spce -ignh I got following error. Fatal error: Atom OXT in residues GLU 69 was not found un rtp enrty GLU with 15 atoms while sorting atoms. Here I am sending a link which has the coordinate file. https://drive.google.com/file/d/0B5HyqLWajWjHWjMyY25Cc3lSRTA/view?usp=drive_web Kindly tell me how to solve this error. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to solve OXT atom (termial oxygen atom) issue?
First of all I am extremely sorry for my mistake. I haven't sent you the modified coordinate file. I have peptide with 69 residues and some of the SER and THR residues are phosphorylated and also some of the missing residues(1 to 6; 36 to 41 and 69) have been modeled by modeller . I have chosen charmm36 force field. When I executed the command pdb2gmx -f 1th1.pdb -o 1th1_processed.gro -water spce -ignh I got following error. Fatal error: Atom OXT in residues GLU 69 was not found un rtp enrty GLU with 15 atoms while sorting atoms. I have checked the rtp file and it does not have the terminal oxygen atom GLN. Then I have checked c.tdb file and I found the following information. [ None ] ; CHARMM CTER [ COO- ] [ replace ] C C CC12.011 0.34 O OT1 OC15.9994 -0.67 OXT OT2 OC15.9994 -0.67 [ add ] 2 8 OT C CA N OC 15.9994 -0.67 -1 [ impropers ] C CA OT2 OT1 What I understand here is that the OXT atom is to be replaced by OT2 and add the information to the rtp file. Am I right? Internally, pdb2gmx re-maps any reference to the OXT atom to one named OT2. No changes are made to the .rtp file and you certainly don't need to change anything. Please upload your coordinate file somewhere and provide a URL. I cannot reproduce the problem with a simple test system. A peptide that I have with a C-terminal GLN works fine with either O/OXT or OT1/OT2. -Justin As Justin asked me coordinate file, I have provided below the link of my coordinate file https://drive.google.com/file/d/0B5HyqLWajWjHU3J3RW9PalhKZ1E/view?usp=drive_web Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to solve the terminal oxygen atom issue (OXT atom) ?
Dear gromacs users, I have peptide with 69 residues and some of the SER and THR residues are phosphorylated and also some of the missing residues(1 to 6; 36 to 41 and 69) have been modeled by modeller . I have chosen charmm36 force field. When I executed the pdb2gmx I got following error. Fatal error: Atom OXT in residues GLU 69 was not found un rtp enrty GLU with 15 atoms while sorting atoms. I have checked the rtp file and it does not have the terminal oxygen atom GLN. Then I have checked c.tdb file and I found the following information. [ None ] ; CHARMM CTER [ COO- ] [ replace ] C C CC12.011 0.34 O OT1 OC15.9994 -0.67 OXT OT2 OC15.9994 -0.67 [ add ] 2 8 OT C CA N > >OC 15.9994 -0.67 -1 [ impropers ] C CA OT2 OT1 What I understand here is that the OXT atom is to be replaced by OT2 and add the information to the rtp file. Am I right? Internally, pdb2gmx re-maps any reference to the OXT atom to one named OT2. No changes are made to the .rtp file and you certainly don't need to change anything. Please upload your coordinate file somewhere and provide a URL. I cannot reproduce the problem with a simple test system. A peptide that I have with a C-terminal GLN works fine with either O/OXT or OT1/OT2. -Justin As Justin asked me coordinate file, I have provided below the link of my coordinate file https://drive.google.com/file/d/0B5HyqLWajWjHalJ0N0lFSEhHcmM/view?usp=drive_web Kindly help me how to solve it? Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to solve the OXT atom (terminal O atom) issue?
Dear gromacs users, I have peptide with 68 residues and some of the SER and THR residues are phosphorylated. I have chosen charmm36 force field. When I executed the pdb2gmx I got following error. Fatal error: Atom OXT in residues GLN 68 was not found un rtp enrty GLN with 17 atoms while sorting atoms. I have checked the rtp file and it does not have the terminal oxygen atom GLN. Then I have checked c.tdb file and I found the following information. [ None ] ; CHARMM CTER [ COO- ] [ replace ] C C CC12.011 0.34 O OT1 OC15.9994 -0.67 OXT OT2 OC15.9994 -0.67 [ add ] 2 8 OT C CA N OC 15.9994 -0.67 -1 [ impropers ] C CA OT2 OT1 What I understand here is that the OXT atom is to be replaced by OT2 and add the information to the rtp file. Am I right? And also for your information I am giving you terminal residue atom information. ATOM526 N GLN68 12.276 4.312 -14.581 1.00 75.07 N ATOM527 CA GLN68 12.290 4.235 -13.157 1.00 75.07 C ATOM528 C GLN68 11.301 3.123 -12.798 1.00 75.07 C ATOM529 O GLN68 11.761 2.088 -12.249 1.00 75.07 O ATOM530 CB GLN68 11.837 5.542 -12.486 1.00 75.07 C ATOM531 CG GLN68 12.065 5.756 -11.011 1.00 75.07 C ATOM532 CD GLN68 11.217 4.937 -10.053 1.00 75.07 C ATOM533 NE2 GLN68 11.740 3.726 -9.682 1.00 75.07 N ATOM534 OE1 GLN68 10.121 5.317 -9.679 1.00 75.07 O ATOM535 OXT GLN68 10.085 3.305 -13.052 1.00 75.07 O1- TER 536 GLN68 Kindly help me how to solve it. Thanks in advance, Surya Graduate student India. -- 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] Force filed for phosphorylated residues
Dear Mark, I have used the charm36 force field. In c.tdb following atoms are there. ; CHARMM CTER [ COO- ] [ replace ] C C CC12.011 0.34 O OT1 OC15.9994 -0.67 OXT OT2 OC15.9994 -0.67 [ add ] 28OT C CA N OC 15.4 -0.67-1 [ impropers] C CA OT2 OT1 and in rtp file for GLN with other atoms they mentioned only one 'O' atom. They didn't give the terminal O atom information. Kindly tell me how to overcome this problem. Thanks in advance Surya Hi, What atoms do you have in that residue, what's in the c.tdb and .rtp for GLN in force field and what did you choose for termini? Mark I have one protein with phosphoserine and phosphothreonine. I want to do simulation, but I do not know which force field I have to use. None of the force field from gromacs has the information of phospho residues. Then I tried with charm36, but did work. Kindly suggest me what I can do. Well, CHARMM36 has everything you need included, so unless you explain what "didnot work" means (because it's the single most useless phrase in debugging anything), there's little anyone can do to help you. Please describe exactly what the problem was (commands, output, errors, etc). -Justin Dear Justin, I solved the problem. That is only the mismatching of residue names and I renamed the residues in my PDB file. Now the problem is with OXT atom at C-terminal end.I other words the exact error is "Atom OXT in residue GLN 68 was not found in rtp entry GLN with 17 atoms while sorting the atoms ". I understood the error. rtp file does not have the atom OXT information. How could one solve this problem? Surya Graduate student India. -- 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] Force field for phosphorylated residues
Dear gromacs users, I have one protein with phosphoserine and phosphothreonine. I want to do simulation, but I do not know which force field I have to use. None of the force field from gromacs has the information of phospho residues. Then I tried with charm36, but did work. Kindly suggest me what I can do. Well, CHARMM36 has everything you need included, so unless you explain what "didnot work" means (because it's the single most useless phrase in debugging anything), there's little anyone can do to help you. Please describe exactly what the problem was (commands, output, errors, etc). -Justin Dear Justin, I solved the problem. That is only the mismatching of residue names and I renamed the residues in my PDB file. Now the problem is with OXT atom at C-terminal end.I other words the exact error is "Atom OXT in residue GLN 68 was not found in rtp entry GLN with 17 atoms while sorting the atoms ". I understood the error. rtp file does not have the atom OXT information. How could one solve this problem? Thanks in advance Surya Graduate student India. -- 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] forcefield for phosphorylated residues
Dear gromacs users, I have one protein with phosphoserine and phosphothreonine. I want to do simulation, but I do not know which force field I have to use. None of the force field from gromacs has the information of phospho residues. Then I tried with charm36, but did work. Kindly suggest me what I can do. Thanks in advance Surya Graduate student India. -- 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] story behind the PCA
Dear gromacs users, I have gone through many tutorials and I didn't get much about principal component analysis(PCA) in gromacs. Kindly some one tell me the story behind the PCA and whats the relation between PCA and free energy landscape? Thanks in advance Surya Graduate student India. -- 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] doubt in PCA?
Dear gromacs users, I just want calculate the free energy difference between two successive trajectories. As I know first we have to generate contrivance matrices by using gmx covar and then have to execute the gmx anaeig for eigenvector analysis. Here my doubt is how to give my interest of trajectories? Suppose I want to have the free energy difference between conformational sub state at 29800ps and conformational substate at 29900ps trajectory. How do I select these two substaes in gmx covar and gmx anaeig? Kindly help me in this regard. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to find energy barrier between two cluster centroids?
Dear gromacs users, I have done 100ns simulation for a peptide with 50 residues length and I generated clusters. Now I would like to calculate the energy difference between two cluster centroids. I have gone through some tutorials and I could not find how to find free energy difference. Kindly tell me how to find the free energy difference between two centroids. Thanks in advance Surya Graduate student India. -- 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] RMSD of energy minimized structure
Dear gromacs users, I have done energy minimization of clustered PDBs. When I try to calculate the RMSD between the minimized clustered PDB and the starting structure of MD simulations I got the following warning. If there are molecules in the input tarjectory file that are broken across periodic boundaries, they cannot be made whole (or treadted as whole) without you providing a run input file. I did not get what does it mean. I have not get any output for RMSD. Where I did wrong? Kindly tell me. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to fix RMSD cutoff in clustering
Dear gromacs users, After my 100ns simulation I want to do clustering. When I look into the gromacs functions I got gmx cluster. This function do clustering based on RMSD cutoff. I searched literature for how to fix RMSD cutoff. I could not find it. Kindly tell me on which criteria we can fix the RMSD cutoff in gmx cluster. Thanks in advance Surya Graduate student India. -- 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] energy minimization
Dear gromacs users, I have done simulations for 100ns. I would like to do energy minimization by using trajectory file which I got after production phase. Can I do energy minimization passing the trajectory file to -c argument? If it is yes, then tell me how to do it. Thanks in advance Surya Graduate student India. -- 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] Interest of c alpha atoms for least square fitting?
Dear gromacs users, Can I give my interest of c alpha atoms for least square fitting in gmx rms for RMSD calculation? Thanks in advance Surya Graduate student India. -- 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] Doubt in gmx rms
Dear gromacs users I have executed the following command for the calculating the RMSD of a protein. gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx My doubt is whether I did correct or wrong I don't know. I have simulation of 197 residues length protein and I want to calculate the RMSD for 2-27 residues. Then I created the index file which contains the c alpha atoms numbers and passed it to RMSD calculation with the -n argument. Just tell me whether my command is correct or wrong. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how does gmx rms work?
Dear gromacs users, Previously I posed a problem how to calculate the RMSD of our interested region of protein, even though I did simulation for full length protein. I got solution from one of our user. Based his suggestion I created index file and have executed the following command. gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n index.ndx My index.ndx file has the c alpha numbers which I have to calculate the RMSD. Here I am not mentioning any superimposition. How does the gmx rms command work? can I do superimposition of my interested residues? and also what is -fit argument? I request you to answer my question. Surya Graduate student India. -- 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] RMSD of interested region?
Dear gromcas users, I have done simulations for 100ns for protein of my interest. The protein length is 197 residues and I fixed the positions one n-terminal residue and from 28th residue to 197 residues also fixed. My interest of area in protein is from 2 to 27 residues. Although I have done simulations for complete length of protein. I just want calculate the RMSD values for region between 2 to 27. If I use reference structure md_0_1.tpr, it gives RMSD for entire protein. But how to find RMSD for my interest of region (2 - 27 residues)? Kindly guide me how to do it. Thanks in advance Surya Graduate student India. -- 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] gromacs.org_gmx-users Digest, Vol 148, Issue 102
Sub: Segmentation fault Dear Justin and Vivek, I came to know what was my fault. I added the refcoordscale = com in .mdp file and it going fine. I have through the many references for refcoordscale, despite of some information I am not getting what exactly it is? Kindly give me some hit. Surya Graduate student India. On Sun, Aug 28, 2016 at 3:30 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Re: Segmentation fault (Justin Lemkul) >2. gmx: malloc(): memory corruption (Quyen V. Vu) >3. KALP-15 tutorial (Roshan Shrestha) > > > -- > > Message: 1 > Date: Sat, 27 Aug 2016 22:17:13 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Segmentation fault > Message-ID: <960b62bc-d72d-9ad7-4625-e2c279df5...@vt.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 8/27/16 5:32 PM, vivek naik wrote: > > I don't think you can do a simulation with pressure if you have position > > restraints, except if your restrained atoms are all in the same plane. > > This is not true. > > > However, ref_coordscaling option should be 'com', which should make it > > better than it is now. > > > > "com" is just one possible option, but it is probably the most stable in > most cases. > > > Also, there is no way isotropic pressure is going to work. it has to be > > anisotropic (xy and z, with the first one being kept to zero). > > > > Anisotropic means all box vectors can vary independently and is usually > applied > to crystals or other solid materials. Coupling xy and z separately is > semiisotropic and is usually used with membranes and surfaces. For a > simple > aqueous protein system, isotropic is in fact correct. > > -Justin > > > Vivek > > > > On Sat, Aug 27, 2016 at 12:15 PM, Seera Suryanarayana < > paluso...@gmail.com> > > wrote: > > > >> Dear gromacs users, > >> > >> I have done mdrun for 10ns with position restrain of interest of our > >> residues. Here I woulk like to explain how I did the position restrain. > >> > >> During gmx pdb2gmx command we usually get posre.itp file which we use in > >> the equilibrium process to restraint the protein. As I want to do real > >> mdrun with restraint on some residues, I just edited the posre.itp file > and > >> kept the restrain information only for residues of my interest and I > define > >> in the md.mdp file as "define =_DPOSRES ; position restrain the > >> protein". I haven't anything to the topology file. When I executed the > >> grompp command I got following warning and then error. > >> > >> WARNING 1 [file md.mdp]: > >> you are using pressure coupling with absolute positions restraints, this > >> will give artifacts. use the refcoord_scaling option and the error was > too > >> many wanrings[1], gmx terminated. Then I executed grompp with the > -maxwarn > >> 1. After preprocessing I did simuations for 10ns. When I try to remove > the > >> PBC with trjconv command I got segmentaion fault error. I request you to > >> tell me What I did wrong and how to resolve it? > >> > >> Thanks in advance > >> Surya > >> Graduate student > >> India. > >> -- > >> 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] Fwd: The results of your email commands
Surya Graduate student India. -- Forwarded message -- From: <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> Date: Sat, Aug 27, 2016 at 12:39 PM Subject: The results of your email commands To: paluso...@gmail.com The results of your email command are provided below. Attached is your original message. - Results: Ignoring non-text/plain MIME parts - Unprocessed: I want to do postion restrain to two residues in my protein of interest. When I look into the genrestr command it is not showing for specific residues. So how can I generate position specific to residuses of our interest? Thanks in advance Surya Graduate student India. - Done. -- Forwarded message -- From: Seera Suryanarayana <paluso...@gmail.com> To: gmx-users-requ...@gromacs.org Cc: Date: Sat, 27 Aug 2016 12:39:45 +0530 Subject: How to do position restrain to particular residues? Dear gromacs users, I want to do postion restrain to two residues in my protein of interest. When I look into the genrestr command it is not showing for specific residues. So how can I generate position specific to residuses of our interest? Thanks in advance Surya Graduate student India. -- 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] Segmentation fault
Dear gromacs users, I have done mdrun for 10ns with position restrain of interest of our residues. Here I woulk like to explain how I did the position restrain. During gmx pdb2gmx command we usually get posre.itp file which we use in the equilibrium process to restraint the protein. As I want to do real mdrun with restraint on some residues, I just edited the posre.itp file and kept the restrain information only for residues of my interest and I define in the md.mdp file as "define =_DPOSRES ; position restrain the protein". I haven't anything to the topology file. When I executed the grompp command I got following warning and then error. WARNING 1 [file md.mdp]: you are using pressure coupling with absolute positions restraints, this will give artifacts. use the refcoord_scaling option and the error was too many wanrings[1], gmx terminated. Then I executed grompp with the -maxwarn 1. After preprocessing I did simuations for 10ns. When I try to remove the PBC with trjconv command I got segmentaion fault error. I request you to tell me What I did wrong and how to resolve it? Thanks in advance Surya Graduate student India. -- 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] g_cluster or g_clustsize
Dear Gromacs Users, I would like to do clustering of my trajectories. When I look into gromacs tool for clustering, I got g_cluster which is based on the RMSD and the other one is g_clustsize which computes the size distributions of molecular/atomic clusters in the gas phase. Mine is protein in solvent system. Here I got confusion whether I use the g_clustsize. Which one I have to use, either g_cluster or g_clustsize? Kindly suggest me. Thanks in Advance, Surya Graduate student India. -- 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] gromcas installation
Dear users, I have centos 6.6 server with 64 processors. I want to do parallel simulations by enabling the MPI threads. For installation of gromacs can I follow the typical gromacs installation guide which is available in the installation instructions? Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] protein has broken after 100ns simulation
Dear gromacs users, I have simulated protein for 100ns. When I visualized the protein in VMD, I have seen the protein into different fragments. Later I came to know that there is no breaking phenomena in simulations and that is because of the PBC problems. I have executed the trjconv command with following arguments to solve the problem, but I couldn't make it successful. I also attached the snapshot. Kindly guide me how to resolve problem? gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -center -pbc mol -ur compact Surya Graduate student India. -- 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] Extension of simulations
Dear users, I have extended my simulations from 20ns to 40ns and I concatenated the .xtc files by using trjcat. I would like to use the concatenated file for further analysis such as rmsd and radius of gyration. We need to have two input files for rmsd analysis. one is .xtc(trajectory file) and other one is .tpr file. But we cannot concatenae the .tpr files by trjcat command. How do I get the extended .tpr file (previous tpr file and extended tpr file). What should I do? Thanks in advance Surya Graduate student India. -- 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] Problem in rmsf calculation
Dear gromacs users, After mdrun I have plotted the rmsf for C-alpha atoms. My protein has 143 C-alpha atoms and I expected only that number in the plot. But I got rmsf values for all atoms of the protein(more than 2250 atoms). I have attached the plot for more information. What could be the reason? Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to fix the ends of the protein?
Dear Gromacs users, I would like to simulate the topological domain of one protein. For that I need to fix the ends of the simulated protein. How do one can fix(constraint) the ends of the protein? Kindly help me how to do this fixation? Surya Graduate student India. -- 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] Introduction of mutation into a PDB file, how?
Dear Gromacs users, I would like to introduce mutation into a pdb file which is going to be used for md simulations. Kindly suggest me the software otherthan SPDV. thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to fix miising atoms in a pdb file?
Dear gromacs users, I have one pdb file which does not have one atom and I need to be fixed that atom in the pdb to run MD simulations. Kindly suggest me to how to fix it. Can I mutate the residue of my interest with the same residue by using pymol or SPDBV to fix the missing atoms? Thanks in Advance Surya Graduate student India. -- 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] Getting too much time to finish nvt equilibrium, why?
Dear Gromacs Users, After energy minimization I have done nvt equilibrium for 1ns. It has taken 15 to 20 minutes when I done it previously. Same equilibrium I did day before yesterday and it has take almost one day. I have used the same work station in both equilibrium processes. I have used the following mdp file. System consists 129 residue length protein and more the three 3,00,000 water molecules. Kindly check the mdp file and let me how to resolve this long lasting processes. define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10.0 ps nstvout = 5000 ; save velocities every 10.0 ps nstenergy = 5000 ; save energies every 10.0 ps nstlog = 5000 ; update log file every 10.0 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm= lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed Thanks in advance Surya Graduate student India. -- 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] Warning in the em.
Dear Gromacs Users, After my energy minimization I got the following info. I would like to know does it mean. I came to know that my em process is not perfect. Kindly tell me how resolve this problem. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 2297 steps, but did not reach the requested Fmax < 1000. Potential Energy = -1.8318672e+07 Maximum force = 2.9344773e+03 on atom 213 Norm of force = 8.8386917e+00 NOTE: The GPU has >20% more load than the CPU. This imbalance causes performance loss, consider using a shorter cut-off and a finer PME grid. NOTE: 15 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) gcq#384: "I do not believe continuum electrostatics" (Arieh Warshel, Nobel lecture 2013) Thanks in Advance Surya Graduate student India. -- 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] Script to submit the md simulations on cluster.
Dear gromacs users,
I would like to submit the mdrun on cluster. I have written a shell script
for submission as following.
EXECUTABLE=./mdrun_mpi465
ARGUMENTS = -v -deffnm md_0_1.tpr
INPUT_FILES = file:///home/suryanarayana1599/md.mdp,
file:///home/suryanarayana1599/npt.cpt,
file:///home/suryanarayana1599/npt.gro,
file:///home/suryanarayana1599/md_0_1.tpr,
file:///home/suryanarayana1599/topol.top
OUTPUT_FILES = md_0_1.trr,md_0_1.xtc,md_0_1.cpt
STDIN_FILE = /dev/null
STDOUT_FILE = ${JOB_ID}.out
STDERR_FILE = ${JOB_ID}.err
REQUIREMENTS = HOSTNAME=ggblr.garudaindia.in(this is cluster name)
TYPE=mpi
NP = 10
OUTPUT_FILES = 2000
Could any one tell me that whether the script is right.
Thanks in Advance
Surya
Graduate student
India.
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[gmx-users] End to end fixing
Dear Gromacs users, I have one protein which has the topological domain with two trans membrane domains. I would like to simulate the topological domain present in the cytosol. But here I can't do simulations as normals proteins. Because as the topological domain has trans membrane domains both sides, which suggests me that the ends should be fixed during simulations. The question is How do we fix the ends? means what should be the distance between the end? To solve this question I have looked into the NMR structure of the protein in PDB. The protein has 20 different conformational states. I checked the distance between the N'-terminal C-alpha and C'-terminal C-alpha. All the conformations showing large variance. How could I solve end-to-end fixing? Kindly tell me what can I do. Thanks in advane Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to remove the water molecules?
Dear gromacs users I have simulated a protein for 500ns in solvent system. I want to remove water molecules from the system to further analysis. I have gone through the manual, but I couldn't find how to remove water molecules. Kindly tell me how can I do it. Thanks in Advance Surya Graduate student India. -- 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] Can't load converted trajectory on to vmd
Dear gromacs users I have executed the trjconv command for generating the .xtc file to futher analysis. I have selected protein for output. I loaded the .gro file on to vmd and then I tried to load .xtc file on to vmd. But, I couldn't load it and I got the following error. vmd Info) Using plugin gro for structure file /Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1.gro Info) Using plugin gro for coordinates from file /Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1.gro Info) Determining bond structure from distance search ... Info) Analyzing structure ... Info)Atoms: 35183 Info)Bonds: 24477 Info)Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0 Info)Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info)Residues: 10932 Info)Waters: 10738 Info)Segments: 1 Info)Fragments: 10742 Protein: 1 Nucleic: 0 Info) Finished with coordinate file /Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1.gro. ERROR) BaseMolecule: attempt to init atoms while structure building in progress! ERROR) Invalid number of atoms in file: 2966 Info) Using plugin xtc for coordinates from file /Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1_noPBC.xtc ERROR) Incorrect number of atoms (2966) in ERROR) coordinate file /Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1_noPBC.xtc Info) Finished with coordinate file /Extended/Dynamics/Hub_simulation/Gpu_md/1ycs/500ns/tmp/md_0_1_noPBC.xtc. Based on above information what I understood is that the .gro file has 35183 atoms including solvent atoms. But in .xtc file has only protein atoms as I have selected protein as output during trjconv execution. Actually I want to load only protein molecule on to vmd after mdrun. Kindly tell me how to overcome this problem. Thanks in Advance Surya Graduate student India. -- 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] During mdrun my protein moves towards edges
Dear gromacs users I have been running the real mdrun after equilibration. mdrun has been submitted for 500ns. After some time(150ns) the protein moves towards edges. I want the internal moments only, but whole protein moves all sides of box rather than at centre of the box. Kindly tell me how to overcome above mentioned problem and what could be the reason? Thanks in Advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How do we calculate free energy of simulated protein
Dear gromacs users I would like to calculate the free energy of simulated protein, how does it can be done? Surya Graduate student India. -- 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] Unable to install gromacs
Dear Gromacs Users We have been trying to install gromacs-5.0.4 on ubuntu 14.04 work station. We have installed all the prerequisites for the gromacs and whenever exicuting the cmake .. we got following error. - The C compiler identification is unknown -- The CXX compiler identification is unknown CMake Error at CMakeLists.txt:45 (project): The CMAKE_C_COMPILER: /usr/share/openmpi/mpicc is not a full path to an existing compiler tool. Tell CMake where to find the compiler by setting either the environment variable CC or the CMake cache entry CMAKE_C_COMPILER to the full path to the compiler, or to the compiler name if it is in the PATH. CMake Error at CMakeLists.txt:45 (project): The CMAKE_CXX_COMPILER: /usr/share/openmpi/mpicxx is not a full path to an existing compiler tool. Tell CMake where to find the compiler by setting either the environment variable CXX or the CMake cache entry CMAKE_CXX_COMPILER to the full path to the compiler, or to the compiler name if it is in the PATH. -- Configuring incomplete, errors occurred! See also /home/rahul/Software/Gromacs/gromacs-5.0.4/build-gromacs/CMakeFiles/CMakeOutput.log. See also /home/rahul/Software/Gromacs/gromacs-5.0.4/build-gromacs/CMakeFiles /CMakeError.log. We didn't get what the error meaning. Kindly help us to overcome from the above mentioned error. Thanks in advance Surya Graduate student India. -- 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] Define box size
Dear gromacs user I have one protein with 254 residues. I would like to simulate this protein in solvent system. For that first we need to define box by editconf. My question is how does we define box size? Surya Graduate student India. -- 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] Why the rmsd value has been varied from different hardware for same protein?
Dear Gromacs Users I have done simulation of one protein in different computers such as GPU(tesla C2075), cpu and cluster(two different nodes with 32 processors) for 5ns. I got different rmsd values for the same protein, but I used same minimized structure in all the computers. My question is what could be the reason for the different rmsd? You can find the rmsd graph in the attachment. Surya Graduate student India. -- 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] gromacs.org_gmx-users Digest, Vol 128, Issue 1
Dear Mark I have used the following command. gmx rms -s em.tpr -f em.trr -o rmsd.xvg I got nothing the graph. You can find the graph in the attachment Surya Graduate student India. On Mon, Dec 1, 2014 at 4:24 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: Electrostatic force cutoffs (Mark Abraham) 2. Position Restraint or remove COM from DNA (Hovakim Grabski) 3. Re: Position Restraint or remove COM from DNA (Justin Lemkul) 4. Can we calculate rmsd from after energy minimization? (Seera Suryanarayana) 5. Re: Can we calculate rmsd from after energy minimization? (Mark Abraham) 6. error in PME mesh load (RINU KHATTRI) 7. Re: error in PME mesh load (Mark Abraham) -- Message: 1 Date: Sun, 30 Nov 2014 20:45:12 +0100 From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] Electrostatic force cutoffs Message-ID: camnumatwkfzm+wx-w_k6olheowuhe894com5klzpmbhnz3r...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, On Sun, Nov 30, 2014 at 6:47 PM, Nathan K Houtz nho...@purdue.edu wrote: Hello all, I'm wondering if gromacs will allow me to use either a wolf electrostatic cutoff method or a damp shifted force cutoff method, similar to what is described by C. J. Fennell (2006). (I think the paper is: http://scitation.aip.org/content/aip/journal/jcp/124/23/10.1063/1.2206581) I'm not familiar with any of the above, but if it involves only two-body interactions, then it is straightforward to implement with tabulated interactions without touching the code (currently only available with the group cut-off scheme). If it involves anything else, and is not an easily expressed modification of something you can find in the manual, then it is probably prohibitively difficult. I guess that's your homework :-) If so, are there any tutorials or how-to's on how to implement them? No. Implementing a high-performance MD implementation is invariably a custom job, but if you can answer the above questions, then we can point you in the right directions. Mark If it matters, I am attempting to simulate tetrolic acid (also called 2-butynoic acid) in a solution of water (Tip3p). Thanks very much for your help! N.H. -- 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. -- Message: 2 Date: Sun, 30 Nov 2014 20:27:29 + (UTC) From: Hovakim Grabski hovakim_grab...@yahoo.com To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: [gmx-users] Position Restraint or remove COM from DNA Message-ID: 346439401.1728836.1417379249165.javamail.ya...@jws10027.mail.ne1.yahoo.com Content-Type: text/plain; charset=UTF-8 Dear Gromacs Users,I'm trying to run a simulation between a Dickerson dodecamer(12 basepair DNA) and 6 molecules of Methylene Blue.My ?1 question is: If I try to ?remove COM from DNA, it gives an error, so I have to set?comm_grps ?= System, but?1) doesn't that affect the Methylene Blue molecules?2) is there any way to ?remove COM from DNA without getting an error? 2. Or should I just use position restraint on DNA's 5' and 3' ends on one strand? Thanks in advance,Hovakim -- Message: 3 Date: Sun, 30 Nov 2014 16:08:18 -0500 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org, Hovakim Grabski hovakim_grab...@yahoo.com Subject: Re: [gmx-users] Position Restraint or remove COM from DNA Message-ID: 547b8742.5080...@vt.edu Content-Type: text/plain; charset=utf-8; format=flowed On 11/30/14 3:27 PM, Hovakim Grabski wrote: Dear Gromacs Users,I'm trying to run a simulation between a Dickerson dodecamer(12 basepair DNA) and 6 molecules of Methylene Blue.My 1 question is: If I try to remove COM from DNA, it gives an error, so I have to set comm_grps = System, but 1) doesn't that affect the Methylene Blue molecules?2
[gmx-users] How to overcome the error Atom P in residue DC 3 was not found in the rtp entry DC5 with 28 atoms while sorting atom.
Dear gromacs users I have been tried to simulate the protein-dna complex. I got error as Atom P in residue DC 3 was not found in the rtp entry DC5 with 28 atoms while sorting atom upon using the command pdb2gmx. I have been added the P atom and bonds of P in the .rtp file which is the part of AMBER99SB-ILDN force field. After the modification of the dna.rtp file I also got the same error which mentioned above. Kindly tell me how to overcome this error. Thanks in advance Surya Graduate Student, India. -- 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] Long bond streches during simulations
Dear gromacs users I have done mdrun upto 50ns by using the command gmx mdrun -deffnm md_0_1 -nt 7. I have total 8 threads and I used 7 out of it along with graphic card nvidia tesla 2075. I first thing I would like to know that when I load the .trr or .xtc file after the .gro file into the vmd some bonds stretched very long are being appeared parallel and vertical in red and white color. My question here is Appearing long bond stretches while loading into vmd right or wrong? At the end of the simulation my protein moves towards the side of the box. After some time (frame no. 1564) few residues moves away from protein and some bonds stretched very long being appeared between that residues and rest of protein. Then the bond stretches disappear from the frame number 1900 and again the bond stretch being appeared during rest of the simulation and at the end I got the final trajectory with some long bond stretching between some residues those moved away from the protein and the rest of the protein. Kindly inform me what could be the reason for the long bond stretching? Thanks in advance Surya Graduate student India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to save trajectories of our interest into vmd
Dear Gromacs Users I would like to analyze frame number 150 to 160 out of 1000 frames. I have been trying to load frames of my interest into vmd. But I was not able to do it. Please tell me how to use it. Thanks in advance Surya Graduate student India -- 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] OpenMM Compatibility issues with GPU build
Dear Gromacs users, I have successfully installed a) cudatoolkit_4.2.9_linux_64_ubuntu11.04.run b) devdriver_4.2_linux_64_295.41.run c) gpucomputingsdk_4.2.9_linux.run d) OpenMM 4.1 from Source e) GROMACS 4.6.5 While trying to install / cmake of mdrun-gpu using the standard procedure given in GROMACS site, export OPENMM_ROOT_DIR=path_to_custom_openmm_installation mkdir build_gromacs_gpu cd build_gromacs_gpu cmake .. -DGMX_OPENMM=ON [-DCMAKE_INSTALL_PREFIX=desired_install_path] make mdrun make install-mdrun I have the problem in the cmake step with following error message: -- Enabling native GPU acceleration CMake Error at src/contrib/CMakeLists.txt:49 (message): The OpenMM build is not compatible with the native GPU build -- Configuring incomplete, errors occurred! Should I install a older version of OpenMM like 2.0 or is there any alternative method to build mdrun-gpu ? Thanks 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.
