AMBER Archive (2005)

Subject: AMBER: Targeted MD

From: Whitney Allen (whitneygallen_at_yahoo.com)
Date: Thu Oct 20 2005 - 13:04:31 CDT

Hi Amber users

I am trying to run Targeted MD on Amber, but I am getting some strange oscillatory behavior in the "current RMSD from reference values". Basically the plot looks almost exactly like an underdamped system going to the tgtrmsd value (thus it gets within the target rmsd, then moves away from it, goes back to near the target rmsd, then moves away, ….). Below is an example of one of the files I am running (eq.in). I have adjusted the tgtrmsd value (1-4), tgtmdfrc value (0.005-1), nstlim (up to 2ns), and used different target/reference structures. All give the same behavior (which is also easily seen by viewing the trajectory). Second, depending on what reference structure I target, sometimes I get a vlimit exceeded error. What does this mean and how do I get rid of this? There is little documentation on Targeted MD so please help. Thanks in advance and let me know if I should send my files.

Whitney Hastings

 

(eq.in)

cat <<eof > mdin

  equilibrate the structure

 &cntrl

   imin=0, ntx=5,

   irest=1, ntxo=1,cut=15.0, tempi=300.0,

   ntpr=10, ntwx=10, ntwe=1000,

   nstlim=100000,tautp=2, temp0=300.0,

   dt=0.001, nscm=100,

   igb=1,ntb=0, saltcon=0.5, gbsa=1,

   ntt=1, nsnb=20,offset=0.13,

   itgtmd=1, tgtrmsd=2.0, tgtmdfrc=0.1,

 &end

Group for target

RES 1 76

END

END

eof

 

mpirun -np 2 sander -O \

              -i mdin \

           -o eq.out \

           -p N218_0.prmtop \

           -c cst01.restrt \

           -ref min70.restrt\

           -r eq.restrt \

               -x eq.x

                
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