Hi Tsjerk, >Hi Akansha,
>Either you need to simulate both systems until you >have full >convergence before you can make conclusions regarding >the (dis)similar behaviour Well I can simulate it until convergence but that on a single processor for my system will take several months of computer time. >or you have to test consistently, running replicate >simulations both on one processor and on 16. This is what I was doing. I was running exactly identical simulations on 1 processor and on 16 processors. By identical i mean - same starting structure, velocities taken from the same *.trr file. The only difference was the number of nodes for the production run. >That being said, it is very well possible that even >between two >simulations of the same system under completely >identical conditions, >except for the starting velocities and possibly the >exact starting >structure, you will get two completely different >results. If you're >protein can undergo a conformational change it's >basically a matter of >chance whether you observe it or not. But I give the same velocities and use exactly same starting structure for both simulations. Basically I use the same files for both cases. Only difference lying in the number of processors. I would think that with same intial conditions the calculations should be identical for both cases. >Of course, I don't say it is not related to your >simulation being >distributed over multiple processors. It may be, but >in order to >exclude other effects you have to repeat simulations >and/or work >through the code very carefully. Which version of >Gromacs did you use? I am using Gromacs3.3. It would very helpful if you can please suggest what care should I take in order to exclude other effects when I repeat the simulation. Thanx Akansha >Hope it helps, > >Tsjerk >On 9/18/06, Akansha Saxena <asaxena17 at yahoo.com> >wrote: >> Hello >> >> Has anybody seen a protein becoming unstable on >> parallel nodes while remaining stable on single >>node? >> >> I am running a NPT molecular dynamics simulation. >>The system contains a protein with 141 residues >>surrounded >> by water making the total to 32714 atoms. I ran this >> simulation at two places for 8ns. One as a serial >>job >> and the other as a parallel job on 16 nodes. >> >> The protein remains stable all through for the >>serial >> job but for parallel job the protein opens up after >> 3ns of simulation and is never stable after that. >> >> All other conditions are exactly the same. Any help >> would be highly appreciated. >> >> Akansha >> >> >> >> Akansha Saxena >> Graduate Student >> Department of Biomedical Engineering >> Washington University in St Louis >> >> gmx-users mailing list gmx-users at 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 gmx-users-request at >>gromacs.org. >> Can't post? Read >>http://www.gromacs.org/mailing_lists/users.php >> >-- >Tsjerk A. Wassenaar, Ph.D. >Groningen Biomolecular Sciences and Biotechnology >Institute (GBB) >Dept. of Biophysical Chemistry >University of Groningen >Nijenborgh 4 >9747AG Groningen, The Netherlands >+31 50 363 4336 Akansha Saxena Graduate Student Department of Biomedical Engineering Washington University in St Louis __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list gmx-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
