[gmx-users] multiple chain

Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my -- gmx-users mailing listg

[gmx-users] REMD vs MD

Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] segemntation fault after run do_dssp

the instruction as shown there but it seems that nothing happened..I already gedit the .bashrc for dssp. -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor

[gmx-users] error after grompp

; 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 fo

[gmx-users] system explode when running in MD production

protein in this simulation was explode and results shows it produce a lot of pdb file at the certain step.Can you tell me why it is happened? I have no idea with this situation. -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry

[gmx-users] system explode when running in MD production

HI guys, I got this problem when I running my protein and metal in mix solvent condition. -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative

[gmx-users] the value of pressure is negative

is negative but the others result is okay. Then i just continue the equilibration.gro to proceed with my md production. And the result for the pressure is 1.5 something and its almost 2 bar for average. Is it normal for that? -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational

[gmx-users] interaction with metal

metal and interact it with my protein.Is it possible to do that? -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh

[gmx-users] System killed after genbox

of my calculation? the formula is no.of molecule that need =( [ % need of hfi x density kg/m^3 x size of box m^3] / molecular weight g/mol ) x avogadro number -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Unive

[gmx-users] create topology other solvent

. Unfortunately there are no coordinate that create. I have been told to do it by using amber for charge calculation before can use it in gromacs. Any suggestion to produce this cosolvent with pdb format? Thanks. -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry

[gmx-users] gmx-user : problem with coordinate number

Dear All, My project is about protein simulation in mix-solvent. At first I used pdb2gmx command then editconf for stting up my box. My co-solvent I creat it from PRTDRG server to get pdb and itp file. 1. I get the name of the file is DRG.ITP with capital letter.Then i change it with new name w