Re: [gmx-users] Regarding version of gromacs
Thank you Justin for your suggestion As I run my simulation on supercomputer and there is availability of gromacs-5.1.2 version not 5.1.4. Earlier it had 5.1.4 version but now it has only 5.1.2 version. -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh -- 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 version of gromacs
Dear all, I have run my simulation on gromacs 5.1.4 for 200ns but now I want to extend my simulation to 500ns with gromacs 5.1.2. Is it possible or will there be problem during total simulation of 500ns in my systems. Please give me suggestion regarding this. -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh -- 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 rdf and number of molecules in the FSS of tetramer
Dear user's I have calculated the rdf of urea molecules around the peptides for different concentration of urea and obtained that peak height of first solvation shell (FSS) decreases with increase in concentration of urea. After that I have calculated the number of urea molecules in FSS and found that urea molecules in the FSS increases with concentration of urea. There is no correlation between the peak height of FSS and number of urea molecules. Can anybody suggest me ? what is the reason The command I have used is gmx rdf -f md.xtc -s md.tpr -o rdf.xvg -selrpos whole_res_com -seltype whole_res_com gmx select -f md.xtc -s md.tpr -os number.xvg -select "resname URE and within 0.5 of group protein" -selrpos whole_res_com -seltype whole_res_com -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh -- 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] Regarding high RMSD
Thank for your suggestion Alessandra I have applied the pbc conditions on my system in steps as follows: 1. gmx trjconv -f full_md.xtc -s full_md.tpr -pbc whole -o full_md_whole.xtc 2. gmx trjconv -f full_md_whole.xtc -s first_frame.gro -pbc nojump -o full_md_nojump.xtc 3. gmx trjconv -f full_md_nojump.xtc -s full_md.tpr -pbc mol -ur compact -center -o full_md_mol.xtc After applying all these conditions, peptides of dimer diffusing out of the box, both in opposite direction at the end of the simulation. kindly suggest me what should I do. -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh -- 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 high RMSD
Thank you for your suggestion Alessandra Villa I have applied all types of pbc conditions but my one peptide is diffusing away from another peptide in case of dimer after half of the simulation time and rmsd is coming out 100 Angstrom after that time which is very high. Please suggest me what should I do. -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh -- 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 high RMSD
Dear all, I have calculated the c-alpha RMSD of dimer having 7 residues peptide each by using command gmx rms. But the calculated RMSD 14 Angstorm is very high, although I have applied all pbc conditions. Anybody can suggest me why so much high RMSD is coming or is it possible. -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh -- 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 RDF
Dear all, I have calculated the rdf of urea molecules with different concentrations along the peptide and obtained the result that in first solvation shell at 0.5 nm g(r) value decreases with increase in concentration but when I calculated the number of urea molecules by gmx select at 0.5 nm, it increases with concentration.Is it possible. Anybody can help me why this is happening . I have used this command for calculating urea molecules and averaged over the frames. gmx select -f .xtc -s .tpr -select 'resname URE and within 0.5 of group potein' -os .xvg -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh -- 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] Fatal error
When I am running the pdb2gmx of trehalose.pdb for making a box of certain concentration then an error is occurring residue that 'TRE' not found in residue topology database.Trehalose is not found in forcefield amber99sb-ildn. So,please suggest me what to do -- 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 (core dumped)
when I run gmx mdrun -v -deffnm 5e61_pr for pr.mdp file then there is an error of core dumped.Please suggest what should I do Step 7, time 0.014 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.041436, max 2.491113 (between atoms 3683 and 3684) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 275276 40.80.1007 0.1008 0.1010 406407 73.10.1650 0.1005 0.1010 579580 45.80.1009 0.1015 0.1010 619620 62.30.1014 0.1015 0.1010 702703 90.00.1212 0.1007 0.1010 763764 34.50.1009 0.1008 0.1010 806808 40.90.1010 0.1005 0.1010 958959 40.10.1007 0.1010 0.1010 1075 1076 75.50.1025 0.0998 0.1010 1118 1119 56.60.1016 0.1012 0.1010 1302 1303 62.40.0998 0.1016 0.1010 1435 1436 90.00.1250 0.1002 0.1010 1547 1549 44.80.1010 0.1004 0.1010 1683 1684 61.40.0999 0.1012 0.1010 1803 1804 50.90.1011 0.1010 0.1010 1835 1836 90.00.1821 0.1110 0.1010 1886 1887 38.50.1008 0.1009 0.1010 1894 1895 34.60.1008 0.1008 0.1010 1950 1951 90.00.1439 0.0997 0.1010 1955 1956 38.90.1008 0.1010 0.1010 1966 1967 90.00.1169 0.1006 0.1010 2107 2108 90.00.1197 0.1002 0.1010 2195 2196 36.60.1008 0.1010 0.1010 2310 2311 46.00.1010 0.1015 0.1010 2334 2335 90.00.1770 0.1069 0.1010 2382 2383 33.30.1016 0.1010 0.1010 2483 2484 90.00.1013 0.1193 0.1010 2518 2519 79.80.1026 0.0994 0.1010 2611 2612 90.00.1360 0.1007 0.1010 2670 2671 37.90.1008 0.1008 0.1010 2683 2684 42.80.1007 0.1009 0.1010 2702 2703 90.00.1017 0.1043 0.1010 2726 2727 90.00.1226 0.1011 0.1010 2747 2748 40.20.1007 0.1011 0.1010 2782 2783 33.50.1010 0.1008 0.1010 2803 2804 34.60.1010 0.1010 0.1010 2878 2879 41.90.1010 0.1014 0.1010 2918 2919 85.50.1106 0.0995 0.1010 2958 2959 54.00.1015 0.1013 0.1010 3030 3031 38.90.1010 0.1010 0.1010 3118 3119 34.20.1009 0.1009 0.1010 3147 3148 67.80.1011 0.1017 0.1010 3155 3156 43.00.1006 0.1008 0.1010 3243 3244 69.10.1016 0.1013 0.1010 3507 3508 67.80.1009 0.1018 0.1010 3651 3652 48.70.1012 0.1016 0.1010 3662 3663 90.00.1071 0.1000 0.1010 3683 3684 90.00.1023 0.3526 0.1010 3734 3735 90.00.1015 0.1234 0.1010 3747 3748 53.80.1017 0.1006 0.1010 4043 4045 57.00.1010 0.1010 0.1010 4059 4060 50.40.1012 0.1016 0.1010 4099 4100 55.80.1013 0.1000 0.1010 4102 4103 63.30.1014 0.0999 0.1010 4158 4159 83.20.1038 0.0997 0.1010 Wrote pdb files with previous and current coordinates Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 4.360419, max 264.224396 (between atoms 3683 and 3684) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 275276 42.70.1008 0.1012 0.1010 406407 90.00.1005 0.1578 0.1010 579580 53.10.1015 0.1010 0.1010 619620 58.80.1015 0.1001 0.1010 702703 90.00.1007 0.1220 0.1010 763764 36.20.1008 0.1010 0.1010 806808 39.50.1005 0.1010 0.1010 822823 38.50.1010 0.1010 0.1010 958959 41.90.1010 0.1014 0.1010 1075 1076 83.00.0998 0.1019 0.1010 1118 1119 54.30.1012 0.1002 0.1010 1142 1143 31.50.1009 0.1009 0.1010 1270 1271 37.20.1010 0.1010 0.1010 1278 1279 52.00.1010 0.1010 0.1010 1302 1303 59.80.1016 0.1012 0.1010 1435 1436 90.00.1002 0.1257 0.1010 1547 1549 44.10.1004 0.1011 0.1010 1683 1684 59.60.1012 0.1016 0.1010 1803 1804 51.30.1010 0.1004 0.1010 1835 1836 90.00.1110 0.1776 0.1010 1886 1887 40.00.1009 0.1013 0.1010 1894 1895 35.10.1008 0.1011 0.1010 1950 1951 90.00.0997 0.1473 0.1010 1955 1956 40.60.1010 0.1013 0.1010 1966 1967 90.00.1006 0.1207 0.1010 2035 2037 90.00.1010 0.1330 0.1010 2107 2108 90.00.1002 0.1237
[gmx-users] Segmentation fault (core dumped)
When I am running the gmx mdrun -v -deffnm 5e61_nvt there is an error of core dumped.I have increased the equilibration time but the same error has occured.So,please suggest me what should I do -- 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.
