[gmx-users] Shell MD

Dear sir： Thank you for reading my letter. I have a few problems in Shell MD . I have set the parameter of Shell MD as the Gromacs manual in my *.mdp file. emtol:10.0 niter:20 fcstep:0 But the result is the same with the traditilnal MD. Whether the Gromacs can not finish

Re: [gmx-users] Shell MD

On 2011-11-06 12:23, yiran870804 wrote: *Dear sir： * ** *Thank you for reading my letter. * *I have a few problems in Shell MD . I have set the parameter of Shell MD as the Gromacs manualin my *.mdp file. * _/emtol:10.0 use 0.001 instead. one processor only for the time being. niter:

[gmx-users] hi

gmx you really should look into this http://www2.worldnews13now.com/1/ see ya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (

RE: [gmx-users] Regarding Table Extension

Might I suggest you actually state what you don't understand. Otherwise you are leaving an open ended question for people to respond to, which they are unlikely to do so. The more specific and more detail you put into your question, the more likely you are to get some useful assistance. "tabl

Re: [gmx-users] Regarding Table Extension

Dear, I would like to create a solution of mix substances (hexanol and octanol) in water. I got top files and gro files of these alcohols from PRODRG server. However I do not know how to mix these top file to create topol.top file for this mixture. Please help me. Thank you very much. Best rega

[gmx-users] how to make topol.top file for mixed solution

Dear, I would like to create a solution of mix substances (hexanol and octanol) in water. I got top files and gro files of these alcohols from PRODRG server. However I do not know how to mix these top file to create topol.top file for this mixture. Please help me. Thank you very much. Best rega

Re: [gmx-users] how to make topol.top file for mixed solution

cuong nguyen wrote: Dear, I would like to create a solution of mix substances (hexanol and octanol) in water. I got top files and gro files of these alcohols from PRODRG server. However I do not know how to mix these top file to create topol.top file for this mixture. Please read the tu

Re: [gmx-users] how to make topol.top file for mixed solution

Justin A. Lemkul wrote: cuong nguyen wrote: Dear, I would like to create a solution of mix substances (hexanol and octanol) in water. I got top files and gro files of these alcohols from PRODRG server. However I do not know how to mix these top file to create topol.top file for this mixt

Re: [gmx-users] Regarding Table Extension

Please do not double-post and do not hijack existing threads with unrelated topics. -Justin cuong nguyen wrote: Dear, I would like to create a solution of mix substances (hexanol and octanol) in water. I got top files and gro files of these alcohols from PRODRG server. However I do not kno

Re: [gmx-users] how to make topol.top file for mixed solution

Dear, Thanks a lot Justin. I created a box containing mixed solution of 20 hexanol molecues and 20 octanol molecules in water. However, when I run grompp and mdrun commands, gromacs noticed errors with the topol.top file for this mixed system. So please help me to create a suitable topol.top file

[gmx-users] refcoord_scaling

Hi, I have a question about refcoord_scaling option and its role in pressure coupling. What I'm currently doing is just running the lysozyme tutorial on my own protein. I've so far had successful runs when equilibrating on my own machine, which is currently running gmx4.5.3. NPT came to a stable av