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

[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

[gmx-users] Regarding rdf and number of molecules in the FSS of tetramer

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 archiv

Re: [gmx-users] Regarding high RMSD

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

[gmx-users] Regarding high RMSD

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

[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

[gmx-users] Regarding RDF

, 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

[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 *

[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

[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