Hi Sopna, First, can you attached the crash report of GROMACS 4.5, so we can have a look on it? Second, are you doing EM and PR before you run it using 4.5? Even if you transfer a stable system from 4.0 it might need some equilibration before you actually run MD, specifically if you assign new velocities to atoms.
Cheers, Itamar On 20/10/2011, at 8:40 AM, Sapna Sarupria wrote: > Hello, > > I did change nsttcouple and nstpcouple but the simulations that run in 4.0.5 > are still crashing in 4.5.4. I think it is related to constraints but I am > unable to figure out exactly what is different. I have pasted both my > topology and mdp (updated for 4.5.4) files. Any ideas? I have read through > the manual and it seems like the mdp files does not need any changes, but > perhaps I am missing something. > > Thank you for your help! > > Sincerely, > Sapna > > nstxout = 0000 ; write coords What that mean? You better give a number bigger than 0. > gen_seed = 372340 ; random seed Just a remark, you can use -1 here for a random number base on time and process number. > constraint_algorithm = shake Any reason why not to using LINCS? ----- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu ============================================
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