[gmx-users] Restrict Terminal of protein?

! -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural University Wuhan,Hubei, 430070 PR China ___ gmx-users mailing

[gmx-users] Re:isotropic force constant

Thank you for your advice,I have find define=-DPOSRE in my pr.mdp file, but I don't know which parameter indicate isotropic force constant of 100kjmol-1A-1. Though I use ref_t=300 for my simulation. Dear users: I have a position restrain .mdp file need to set,I use 300K in

[gmx-users] isotropic force constant?

Dear users: I have a position restrain .mdp file need to set,I use 300K in which an isotropic force constant of 100kjmol-1A-1 is applied to all nonhydroggen protein atoms. In my pr.mdp file which parameter I should add? Thank you very much!

[gmx-users] Salt concentration!

Dear users: My protein is large,so I use genbox -shell 1.2 to add water, Then I genion -conc 0.15 -neutral, At last,In .top file I find 7703 water, but there are 183 Na+,170 cl-,I want to know whether ions is too more. Is this normal? Could somebody tell me?

[gmx-users] Re:realloc Error !

Mark: Thank you for your advice,I always get one of these error message, in same situation. I find that when I got box shift error message,there are many lincs warning. I did not find some special message for memory not enough error message. Qiang Zhong : I have a complex protein

[gmx-users] Re:realloc Error !

I have a complex protein which is predicted from cluspro server,I use it as a start structure,I want to know the complex will deformated to a new conformation which is NMR experiment result(it only include a fragment of protein).So I want to know the two protein interaction information by MD.

[gmx-users] realloc Error !

? Thank you very much! -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural University Wuhan,Hubei, 430070 PR China

[gmx-users] genion error!

grompp -f fullmd_sol.mdp -c minimized.gro -p cln.top -o fullmd.tpr mdrun -nice 0 -v -s fullmd.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education

[gmx-users] Add ions on protein

complex of protein and ions to a native ca2+ loaded conformation. Could somebody tell me how to do? Thank you very much! -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences

[gmx-users] LINCS WARNING

0.1000 0.0999 0.1000 .. What happen with it,Is this harm to my result? -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural

[gmx-users] How to display file .xvg,how to use my_dssp

Hollow: My linux can not instal grace,so I don't know to view .xvg file,Could someone tell me some other graphic software. I want to use my_dssp , but I don't know where it is,Could someone tell me where to find it? -- Qiang Zhong Key Lab

[gmx-users] Error:4 atoms are not part of any of the T-Coupling groups

minimized_water.gro -p cln.top -o fullmd.tpr But Error still there. Could somebody tell me how to do? Thank you very much! -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology

[gmx-users] Re:Error:4 atoms are not part of any of the T-Couplinggroups

is that the *groups* included for the tc-grps shall cover all atoms. On 2/7/2007 9:34 PM, Qiang Zhong wrote: Hollow: I have post my question last time,my emailbox can not work, So I post again. I have 4 calcium ions bind at protein, when I use command: grompp -f fullmd_sol.mdp -c