Re: SMD and restart

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Mon Aug 14 2006 - 01:23:12 CDT

Hi Gianluca,

SMD simulation can be restarted. I think the problem arises here because
you did not update the firsttimestep value in your restart file (you set
it up to 0 and it should have been 500000). NAMD computes the location of
the dummy atom as x=vt, with t being the simulated time. Thus, when you
restart the simulation, you need to indicate the appropriate timestep, or
otherwise the dummy atom will be misplaced and huge forces will appear.

Let me know if you need more help,
Marcos

On Sun, 13 Aug 2006, Gianluca Interlandi wrote:

> Dear NAMD users,
>
> I'm performing SMD simulations and I have problems when I restart a
> simulation, i.e., the force on the SMD atom gets huge. These are the last
> 2 lines of the output (grepped for SMD) of the first cycle before the
> restart:
>
> SMD 499990 -49.0427 -29.1025 -6.53669 -217.589 -23.0796 -39.0692
> SMD 500000 -49.0657 -29.1592 -6.48743 -208.553 -22.1211 -37.4467
>
> These are the first two lines of the output after the restart:
>
> SMD 0 -21.9562 -23.8701 6.80649 4826.53 511.947 866.625
> SMD 10 -21.7811 -23.7529 6.80844 4738.6 502.62 850.836
>
>
> I use the following parameters:
>
> SMDk 7
> SMDVel 0.00002 #; Before restart
> SMDVel 0.00008 #; After restart
> SMDDir -0.978939263405 -0.103835396861 -0.175772947075
> SMDOutputFreq 10
>
> As you can see I changed the velocity after the restart. Does this mean
> that it is not possible to restart a SMD simulation? Or is the problem
> that I increased the speed?
>
> Thanks a lot,
>
> Gianluca
>
> -----------------------------------------------------
> Dr. Gianluca Interlandi gianluca_at_u.washington.edu
> +1 (206) 685 4435
> +1 (206) 714 4303
> http://biocroma.unizh.ch/gianluca/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:43:55 CST