Re: [gmx-users] How many ps needs a simulation?
On Wed, 10 May 2006 19:29:26 -0700 (PDT) jahanshah ashkani [EMAIL PROTECTED] wrote: Thanks, In fact I have a sequence with 1277 residue. It is stable even in 50ps. But when I continue to simulation my pc is restarted in 4 steps, automaticly. I should say that this step needs about 100 h time. 50 ps for a protein of 1277 residue is probably equivalent to the first minute of a marathon. The system size you chose can be considered enormous ! Anyway as M and W already said, the simulation length that would give you a reasonable answer depends entirely on what question you want to answer and the quality of the answer you want. From a 50ps simulation you have absolutely no answer at all !! Good luck XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How many ps needs a simulation?
Dallas B. Warren wrote: How many ps needs a simulation? How long is a piece of string? rofl... didn't see until now we both had the same response to this question! Cheers, Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] How many ps needs a simulation?
Mark, rofl... didn't see until now we both had the same response to this question! Yeah, spun me out a bit too when your repsonse arrived after I had sent mine ;-) Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How many ps needs a simulation?
Hi Jahan,You mention your computer restarted. Now that sounds serious. Can you give more details about that? What happens in the log-file before the crash. Was it gromacs or something else that caused it? Are you running windows or *nix? Furthermore, as mentioned before, how long the simulation should be, depends on what you want to get from it. If you try to fold your sequence, I'd guess you need at least 5-10 seconds.., and a few lifetimes of simulation if we don't get much faster computers soon. Still, if you're interested in functional processes, you're facing very long relaxation times, which I estimate could well be about 20-25 ns or more (as I've seen for a quite globular protein of my own, about half the size of yours). That means that before you get some real information you need simulation times of 40-50 ns at least. You can check the relaxation or convergence of your simulation by looking at the cosine content of the principal components (g_anaeig -h). If you're interested in local phenomena, you may be able to get away with shorter time scales. By the way, if your protein is more or less rigid, you can cut down the computational cost by choosing a proper definition of your simulation box. If your interested you can contact me off the list for that (but keep other questions regarded to the simulations directed to the list please). TsjerkOn 5/11/06, Dallas B. Warren [EMAIL PROTECTED] wrote: Mark, rofl... didn't see until now we both had the same response to this question!Yeah, spun me out a bit too when your repsonse arrived after I had sentmine ;-)Catch ya,Dr. Dallas Warren LecturerDepartment of Pharmaceutical Biology and PharmacologyVictorian College of Pharmacy, Monash University381 Royal Parade, Parkville VIC 3010[EMAIL PROTECTED] +61 3 9903 9524-When the only tool you own is a hammer, every problem begins to resemblea nail.___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of Groningen Nijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] How many ps needs a simulation?
How many ps needs a simulation? How long is a piece of string? Seriously though, depends on what you are trying to observe and determine. Also check the literature to see what is currently being done with similar systems and properties. Typically it will be at least an order of magnitude longer than the process you wish to observe. But what is possible and what you want can be very too different things. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] How many ps needs a simulation?
Thanks, In fact I have a sequence with 1277 residue. It is stable even in 50ps. But when I continue to simulation my pc is restarted in 4 steps, automaticly. I should say that this step needs about 100 h time."Dallas B. Warren" [EMAIL PROTECTED] wrote: How many ps needs a simulation?How long is a piece of string?Seriously though, depends on what you are trying to observe anddetermine.Also check the literature to see what is currently being done withsimilar systems and properties."Typically" it will be at least an order of magnitude longer than theprocess you wish to observe. But what is possible and what you want canbe very too different things.Catch ya,Dr. Dallas WarrenLecturerDepartment of Pharmaceutical Biology and PharmacologyVictorian College of Pharmacy, Monash University381 Royal Parade, Parkville VIC 3010[EMAIL PROTECTED]+61 3 9903 9524-When the only tool you own is a hammer, every problem begins to resemblea nail. ___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
