[gmx-users] Re: umbrella sampling (PMF) position discrepancy

2012-09-10 Thread Sheeba
range from 0 to 2. Is that what you get? Sheeba - Sheeba J. Irudayam Postdoctoral Researcher Department of Chemistry University of North Carolina at Chapel Hill isheeba[at]email.unc.edu -- View this message in context: http://gromacs.5086.n6.nabble.com/umbrella-sampling-PMF-position

[gmx-users] Re: Umbrella Sampling Pull code Problem

2012-08-31 Thread Sheeba
ations and I am not sure if what I observed is applicable to version 4.5.3. Sheeba - Sheeba J. Irudayam Postdoctoral Researcher Department of Chemistry University of North Carolina at Chapel Hill isheeba[at]email.unc.edu -- View this message in context: http://gromacs.5086.n6.nabble.com/Umb

[gmx-users] Re: mdrun on GROMACS 3.3.1

2012-08-29 Thread Sheeba
ture might be a cause for this error. Sheeba ----- Sheeba J. Irudayam Postdoctoral Researcher Department of Chemistry University of North Carolina at Chapel Hill isheeba[at]email.unc.edu -- View this message in context: http://gromacs.5086.n6.nabble.com/mdrun-on-GROMACS-3-3-1-tp4458897p5000673

[gmx-users] Re: mdrun on GROMACS 3.3.1

2012-08-28 Thread Sheeba
since there is no mapping section in the itp files it does not actually couple the CG structure and the resulting PE I get are similar to the PE for a regular AA system. This is however my observation and I would appreciate if the developers of the modified 3.3.1 version could check and confirm

Re: [gmx-users] REMD with 'bad contacts' error

2011-07-14 Thread Sheeba Jem
the exact same tpr files when I use 1 processor per replica I get the bad contacts error. Could the remd crashing have been due to some scaling issue? if so, the error in the log files with 'bad contacts' was misleading... Sheeba On Wed, Jul 6, 2011 at 1:06 AM, Mark Abraham wrote:

Re: [gmx-users] REMD with 'bad contacts' error

2011-07-05 Thread Sheeba Jem
erTerm(): TS reports task <1> pid <24584> on host killed or core dumped I attach the mdp file that I used. I would appreciate any other suggestions you might have. Thanks Sheeba On Tue, Jul 5, 2011 at 7:22 PM, Justin A. Lemkul wrote: > > > Sheeba Jem wrote: > >>

[gmx-users] REMD with 'bad contacts' error

2011-07-05 Thread Sheeba Jem
n/mdrun_mpi -s remd.tpr -multi 50 -replex 1000 -deffnm remd I am not sure where I am going wrong and any help is greatly appreciated. Since the size of the mail is too big when I attach the files, the mail bounces therefore I am sending only the input files used for the peptide water system an