From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Jul 18 2013 - 13:26:52 CDT
what about not minimization? If you just minimize for say 500 steps and
then start MD, what happens? This sounds like a problem with your machine,
or your connection to the machine being used.
On Thu, Jul 18, 2013 at 2:14 PM, Rajan Vatassery <rajan_at_umn.edu> wrote:
> There almost has to be an error somewhere. Check the all the files that
> you are writing to, as well as the current working directory and your home
> directory for any possible error outputs. After you find something, repost
> to the list.
> Good luck,
> On Thu, Jul 18, 2013 at 12:42 PM, venkata agasthya <kvagasthya_at_gmail.com>wrote:
>> Hello everybody,
>> I am new to NAMD and VMD. i am presently working on MD simulations on
>> protein/ligand complex. I have problem with the minimization part. I have
>> followed the 18c6 tutorial and developed my files and ran a minimization
>> run of my protein. Minimization ran fine upto 539 steps and it does not go
>> beyond it and also does not show me any error. I tried to increse the
>> number of steps but it did not work out. Can anyone please help me out. The
>> number of steps I used is 1000.
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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