[gmx-users] gromacs

hello users Can anyone tell me that is it necessary to run a long simulation at one tme? or I can do it in parts. Like if i am doing for 1000ps, can i do 500 at one tme and rest in next run? Would it give same results or its a wrong procedure? -- Gromacs Users mailing list * Please search the

Re: [gmx-users] gromacs

Hi, There is no problem in doing the simulation in parts as long as you take care to ensure continuity by using .cpt files, etc. You can concatenate the trajectory in the end for analysis. Regards, On 8/30/14, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: hello users Can anyone tell me that

[gmx-users] Counting Interactions in vacuo ..

Hi all I'd like to count the number of bonding and non-bonding interactions in a one molecule system in vacuo, just for educational purpose. Is there any way to obtain that info in Gromacs..? Thank you very much!! Sergio -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas

[gmx-users] updates about ACPYPE

Dear community, Many thinks for all of you who uses ACPYPE and my sincere apologises for those who have been facing issues when running ACPYPE in “amb2gmx” module to convert to Gromacs files with Amber Forcefields 12SB and 14SB. I am aware of this issue for more than a year, since AmberTools13

[gmx-users] Interuption Simulation

Dear Gromacs users I have submitted a simulation for 10 ns. Now when I started to plot the graphs such as RMSD, I saw that it has stopped at 8 ns. The point is that although the run has stopped before specified time, I see in md.log file the time report for the simulation, the same as report

[gmx-users] Interuption Simulation

Dear Gromacs users I have submitted a simulation for 10 ns. Now when I started to plot the graphs such as RMSD, I saw that it has stopped at 8 ns. The point is that although the run has stopped before specified time, I see in md.log file the time report for the simulation, the same as report

Re: [gmx-users] PMF curve in umbrella sampling

Thankyou for your response. I spaced them at approx 0.05nm because at the 473rd configuration my ligand becomes solvated...and completely dissociated from the protein and there is a jump in the COM distances. Would you recommend running windows for configurations beyond 473 to get an accurate PMF

[gmx-users] 转发：entropy calculation by g_anaeig

Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- 发件人：孙业平 sunyep...@aliyun.com 发送时间：2014年8月30日(星期六) 23:19 收件人：vmd-l vm...@ks.uiuc.edu 主　题：entropy calculation by g_anaeig Dear all, I am using g_anaeig to