There might be some problem during the heating step(I am guessing it). For
every lambda you need not have to heat your system and equilibrate it. You
can use the previous lambda value rst file for the next step and continue
the simulation. Remember you just need a starting structure for any
simulation. It might take a while to get equilibrated. So, you can use
anyone of the good rst file of the charge annihilation step also for the vdw
step. Hope this will slove the problem.
manikanthan
On Tue, May 25, 2010 at 1:43 AM, sunita gupta <sunita.bio.gmail.com> wrote:
> Ya,after visualizing the mdcrd files of for the lambda values for which the
> job is getting crashed, I observed that the ligand is blowing out of the
> water box and also the structure of the ligand is destroyed completely.
> Also, how can I restart the job using charge annihilation step, as the
> lamba
> values for the two steps are not identical?
> For this I thing I will have to setup charge annihilation step for lambda
> value 0.56262 and take it further to vdw decoupling step.
> Kindly guide me.
>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 25 2010 - 09:00:09 PDT
