From: Ragothaman Yennamalli (ymr79in_at_yahoo.co.in)
Date: Mon May 23 2005 - 02:00:38 CDT
Hi Pijush,
Thanks for the solution. It worked perfectly fine. I
would like to know if there is some points that has to
be kept in mind while doing SMD. Like the basis of
selection of the smdatom and fixedatom points. Can we
give more than one smdatom for simulation?
Thanks in advance.
Regards,
Ragothaman
--- Pijush Ghosh <pijush.ghosh_at_ndsu.edu> wrote:
> Hello Ragothaman
> This is a very common problem one faces in NAMD,
> fist thing I would like
> to suggest you is, check the dimensions of your
> ubiquitin molecule in VMD or
> by some other means, then in your configuration file
> see that the periodic
> box size you have used are same or couple of Angs.
> bigger than those. Now
> make your PME grid size also same as those dimension
> (at the same time see
> those values are multiple of 2,3 or 5). Another
> suggestion is while doing
> SMD start with smaller magnitude of force in that
> way you can make sure that
> your system is not turning unstable because of very
> high K.E.
> Hope this helps.
>
> Pijush Ghosh
> PhD Student
> Department of Civil Engineering
> North Dakota State University
> Fargo. ND. 58105. USA
> Phone:
> 701-231-6491(Lab)
> 701-231-4341(Res)
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu
> [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> Of Ragothaman Yennamalli
> Sent: Wednesday, May 18, 2005 12:21 PM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: Error in running tutorial files
>
> Hi all,
>
> I am new to NAMD. I am learning SMD and when I tried
> running SMD using the ubiquitin example, I got the
> following error:
>
> FATAL ERROR: Periodic cell has become too small for
> original patch grid!
> Possible solutions are to restart from a recent
> checkpoint,
> increase margin, or disable useFlexibleCell for
> liquid
> simulation.
>
> I searched the mailing list but they all are
> suggesting to have a water sphere around the
> protein,
> but the tutorial says without water sphere. The
> SMDDir
> is the same as given in the tutorial.
>
> Thanks in advance,
>
> Regards
>
> Ragothaman
>
>
>
> **************************************
> Y. M. Ragothaman,
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Information Technology,
> Jawaharlal Nehru University,
> New Delhi - 110067.
>
> Telephone: 91-11-26717568, 26717585
> Facsimile: 91-11-26717586
> **************************************
>
>
________________________________________________________________________
> Yahoo! India Matrimony: Find your life partner
> online
> Go to: http://yahoo.shaadi.com/india-matrimony
>
>
**************************************
Y. M. Ragothaman,
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Information Technology,
Jawaharlal Nehru University,
New Delhi - 110067.
Telephone: 91-11-26717568, 26717585
Facsimile: 91-11-26717586
**************************************
________________________________________________________________________
Yahoo! India Matrimony: Find your life partner online
Go to: http://yahoo.shaadi.com/india-matrimony
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