[gmx-users] Regarding Table Extension

*Dear All, This is the site where they have mentioned like the sum of the longest diagnol of the box + rlist = table extension http://smog.ucsd.edu/MDP_sample.html Further whatever that was mentioned in the manual I could not understand. I kindly request any one of you to explain me

[gmx-users] pressure scaling more than 1%

Dear teacher, when i do remd in the npt ensemble. it will be bomb when it run a little time . and the dt is 0.00144,(in my opinion ,it is small enough , in this condition , the simlution time is about one month ) how could i do except using a small dt. thanks!! step 112000, will finish Sun Dec 1

[gmx-users] cutting a trajectory and continuing from a part of it

Dear users is there any way I can omit a part of my run and continue again from there on? in fact my protein escaped the box i had introduced to it, after 13ns past. I am searching for a way to bring it back and continue  my run after 13th ns. I do appreciate your kind help. regards, sajad-- gmx

Re: [gmx-users] cutting a trajectory and continuing from a part of it

Sajad Ahrari wrote: Dear users is there any way I can omit a part of my run and continue again from there on? in fact my protein escaped the box i had introduced to it, after 13ns past. I am searching for a way to bring it back and continue my run after 13th ns. I do appreciate your kind h

Re: [gmx-users] pressure scaling more than 1%

杜波 wrote: Dear teacher, when i do remd in the npt ensemble. it will be bomb when it run a little time . and the dt is 0.00144,(in my opinion ,it is small enough , in this condition , the simlution time is about one month ) how could i do except using a small dt. Please consult: http://w

[gmx-users] GB implicit solvent - non polar solvation forces

Hi, I am using the GBSA implementation in GROMACS for running implicit solvent MD simulations. Can someone clarify if the forces computed at each time step include the derivatives of the non-polar solvation energies (the surface-area dependent energy term)?  Best, Hari ===

[gmx-users] fudge QQ values

Hello everyone, I just have a quick question. So the fudgeQQ value for amber99sb force field in gromacs is 0.8333, but I wonder if we should use 0.83 or 0.8333? I quite different simulation results by manipulating this value. In my antibody - ligand system, 0.8333 showed ligand not stable

Re: [gmx-users] fudge QQ values

Yun Shi wrote: Hello everyone, I just have a quick question. So the fudgeQQ value for amber99sb force field in gromacs is 0.8333, but I wonder if we should use 0.83 or 0.8333? I quite different simulation results by manipulating this value. In my antibody - ligand system, 0.8333 s

[gmx-users] Gromacs error message

The below steps were followed to perform the simulation: 1st) a topology file was generated (.top) from the pdb-file (.pdb) by the pdb2gmx program;2nd) the complex was solvated using the programs editconf and genbox. Finally t

Re: [gmx-users] Gromacs error message

Did you create/have any .mdp file called 'minim.mdp' . The grompp is looking for the run parameter file and not finding it as you may not have created one. From: Salvatore Guccione To: gmx-users@gromacs.org Sent: Saturday, November 5, 2011 2:33 PM Subject: [gmx