Re: [AMBER] Problem of RMSd plotting using merged tarjectories

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Tue, 2 Nov 2010 12:21:43 -0700

> I have problems with RMSd plotting using merged two trajectories. Now I
> have done 10ns simulation of Enzyme in water, but I had to restart
> simulation because some hardware problem affected my simulation at middle of
> trajectory (8.2ns). So I made restart file by using PTRAJ and then
> restarted simulation from previous time steps of problem point.

It sounds like you have two simulations with a velocity-less join point:
as soon as you started running with the created restrt file, you would
have begun a new equilibration that would not be a continuous simulation
with the previous run, unless you were also saving velocities to mdvel
and used these in constructing your restrt file.

> My problem is as follows,
> After simulation was done, I combined two trajectories to check the RMSd
> plot of enzyme. But The peak was suddenly dropped at merged time
> steps(8.2ns).
> But when I looked this through VMD, there are no sudden rotating or movement
> at that point(8.2ns).

Perhaps you accidentally started with the original restrt, which I
assume is what you are rms'ing to? Does mdout for the 2nd trajectory
show your temperature starting to warm up again?


AMBER mailing list
Received on Tue Nov 02 2010 - 17:30:02 PDT
Custom Search