SMD and restart

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Mon Aug 14 2006 - 01:01:50 CDT

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.
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